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Advances in Politics and Economics 
ISSN 2576-1382 (Print) ISSN 2576-1390 (Online) 

Vol. 5, No. 1, 2022 
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99 
 

Original Paper 

Religion and Power Comparing Political Landscape in the 

Religious Conflicts in Poso and Maluku 

Sri Yunanto1* & Angel Damayanti2 
1 Graduate School of Political Science, Universitas Muhammadiyah Jakarta, Indopnesia 
2 Department of International Relations, Universitas Kristen Indonesia, Jakarta, Indonesia 
* Sri Yunanto, Graduate School of Political Science, Universitas Muhammadiyah Jakarta, Indopnesia 

 

Received: January 4, 2022     Accepted: January 21, 2022     Online Published: January 28, 2022 

doi:10.22158/ape.v5n1p99          URL: http://dx.doi.org/10.22158/ape.v5n1p99 

 

Abstract 

Indonesia is a pluralistic country inhabited by Muslims, Christians, Catholics, Hindus, Buddhists, and 

Confucians, with Muslims, hold the majority population. Their adherents live in harmony and tolerance 

within the democratic political system. However, at the outset of the reform era, Indonesian people 

suffered from instabilities, conflicts, and terrorism, capitalizing ethnic, tribal, and religious symbols for 

political objectives such as those in the religious conflicts in Poso and Maluku. This paper seeks to 

compare the political landscape of the Muslim-Christian conflicts in Maluku and Poso. This research 

uses a qualitative approach with a comparative method and finds similarities and differences of political 

factors explaining the conflicts. Its similarities were conflicts amongst social, political, and military 

leaders at the national and local levels. In addition, they used agent provocateurs to provoke their 

co-religionists. However, this study found differences in the involvement of student and youth unions in 

Maluku but not in Poso. 

Keywords 

conflict, religion, maluku, poso, politics 

 

1. Introduction 

Indonesia is a big pluralistic country. Diverse ethnic, tribes, religious believers live together in harmony 

and tolerance. Bang Ki-moon, UN Secretary-General, in his speech in the Sixth Global Forum of the 

Alliance of Civilizations held on 29 August 2014, testified that Indonesia is a country where thousands of 

ethnic groups have been, for decades, living side by side, in harmony and been able to foster mutual helps 

in resolving social problems. Moreover, international leaders have recognized Indonesian Muslims as the 

majority population, moderate, tolerant and peaceful. 



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However, such a situation does not neglect that tension between internal religious followers and other 

religious followers, notably between Muslims and Christians, never existed in contemporary Indonesian 

history. Specifically, in the beginning years of reform time, religious tensions and conflicts broke up such 

as those happened between Dayak and Madura ethnics in Central Kalimantan, Muslim and Christian 

conflict in Dani and Also tribe in Papua where Muslims came there as migrants and Papuan as the 

indigenous people and also Muslim and Christian conflict in Maluku and Poso which we will discuss in 

this article. These incidences took people’s lives and destroyed their properties and worship places. 

Moreover, it also dotted the peaceful, harmonious, and tolerant life of Indonesian people who enjoy the 

transition of democracy. 

Surprisingly, many scholars view that the primary roots of the conflicts in the New Order time and after 

New Order do not come from diversity and plurality of the people. Instead, they hailed from the 

weakening of the state as the significant explaining factors of the conflict. Within pluralistic and diverse 

characteristics of the Indonesian people, communal conflicts with primordial dimensions remain a severe 

security threat. Further, political events such as general elections that Indonesia experienced would 

trigger factors. Political parties used religious and other primordial brands massively as political tools to 

discredit their rivals, such as had happened in Maluku and Poso conflicts. 

 

2. Significance of the Study, Methodology and Research Questions 

Religious conflicts in Maluku and Poso have now been over, despite terror threats and attacks in Poso 

and the vulnerable situation in Ambon. Nonetheless, the potential of religious conflicts to break up in the 

current and coming Indonesia remains serious. The rising radical movements in many walks of life and 

the political ups and downs are important factors explaining the potentiality of conflicts (bbc.com 2016) 

(Note 1). Radical activists or groups with religious, ethnic, and political backgrounds capitalize on 

religious and other primordial issues, known in Indonesian contexts as ethnic, religion, race, and groups 

(Suku, Agama, Ras dan Antar Golongan/SARA) to achieve their political, cultural or even ideological 

objectives. Social, political, and government leaders have extended alerts and reminders to political 

contestants and their core followers not to capitalize on primordial issues for political objectives. 

Capitalizing on these sensitive issues in our diverse, multi-ethnic, and religious society could bring this 

nation into grave peril. Maluku and Poso conflicts have taught us how political conflicts matter in 

explaining religious conflicts.  

Therefore, discussing political factors or landscape in the religious conflict in Maluku and Poso will be of 

significance to reflect current political events when certain political contestants might use black or 

negative campaigns using primordial sentiments, notably religion. Using qualitative comparative 

approach, with multi-methods data collections such document, media analysis and triangulated with 

interviews, this article seeks to discuss two things: first, the comparison between the nature of the 

conflicts in Maluku and Poso, which cover; their escalation and de-escalation, casualties, Second, the 



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comparison of the political landscape of the conflicts in the two locations. We will analyze the 

similarities and differences between the conflicts and their political factors. 

 

3. Conceptual and Theoretical Notes 

3.1 Religious Conflict 

This research uses two central concepts; religious conflict and political landscape. The concept of 

conflict connotes positive and negative meanings. In its positive meaning, conflicts can be in the form of 

constructive competition. In its negative meaning, as used in this article, conflict is defined as a type of 

competition to win over value, power, or status, yet materialized by physical attacks in terms of injuring, 

attacking, or even killing their adversaries to meet un-negotiable goals of the two or more parties 

(Panggabean & Trijono, 2004) (Note 2). Religious conflicts, as Horowitz asserts, can also be analyzed 

within the concept of ethnic conflict as it is rooted in the ascribed group’s identity such as caste, 

nationality, language, tribes, and religion (Sukma in Snitwongse, Kusuma, & Thomson, 2004; Trijono, 

2004) (Note 3). However, this article defines religious conflict by modifying that of developed by Zulfan 

Tadjoedin, who categorizes religious conflict or violence as a type of communal conflict, that is, violent 

attacks between two religious groups, driven by religious motivation characterized by the capitalization 

of religious symbols (Tadjoedin, 2013) (Note 4). 

3.2 Political Landscape 

From Architectural terminology, the political landscape here means all visible features or characteristics 

of political dynamic, which surround the Maluku and Poso conflicts. Therefore, this article first discusses 

the most important political change commonly termed reformasi (reform), democratization, or 

democratic transition in understanding the political landscape. Theorists like Samuel Huntington (1991), 

Jack Snyder (2003), O’Donel, and Phillip Schmitters have reminded us that democratization produces 

promises for changes and improvement for a better life. However, it occurs in the weakening state, 

characterized by instability, violent conflict, and potentials of revolution in which leaders of the 

conflicting groups are compromising to reach political equilibrium. Unfortunately, a weak state is 

powerless in mobilizing security apparatus to cope with the situation. 

 

4. Result 

4.1 The Comparison between the Nature of Religious Conflict in Poso and Maluku  

4.1.1 The Nature of Religious Conflict in Poso 

This article classifies the Poso conflict into two periods, before the Malino agreement (1998-2002), after 

the Malino agreement (2002-2007), or even today. The classification of the Poso conflict into two 

periods is essential. Before and during the Malino agreement, the communal conflict happened between 

the Muslim and Christian communities in Poso. After the Malino agreement, communal conflict shifted 

to asymmetric conflicts or terrorism using Islamic brands targeting Christian areas, groups, and security 



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apparatus, notably police officers. The two periods of the Poso conflict are then divided into 5 phases as 

laid out in the following Table 1. 

 

Table 1. Phases of Poso Conflict 

Before Malino agreement 

Phase Period -Brief description 

1 1998-1999 - Fighting between Muslim and Christian youths in Poso escalated to the 

mobilization of Christian militia from Tentena and Muslims militias from 

Parigi Moutong to Poso. 

- The segregation of the Morowali region from Poso.  

2 April-May 

2000 

- The mobilization of Muslim and Christian Militias from Poso increased. 

- Christian Church Association (Gereja Kristen Sulawesi Tengah/ GKST) and 

Muslim associations in the conflict started to involve. 

3 May2000-June 

2001 

(Retaliation 

period) 

- Christian militia massively attacked Kilo Sembilan Pesantren, which killed 

70 Muslims. 

- The conflicts spread to all regions, which segregated Muslim and Christian 

areas. 

-Islamic organizations like MUI, Al Khairat, and Muhammadiyah started to 

involve. 

-Terrorist groups came to Poso. 

4 July 2001 - Christian fighters from Tentena attacked Muslims in Poso, killing 14 

Muslims in Buyung Kendo. 

- Laskar Jihad and other Muslim militias arrived in Poso. 

-The conflicting parties reached the Malino agreement 

- After the Malino Agreement (www. Epi.edu, 2009) (Note 5) 

5 2001 

Terror Period 

- Communal conflict relatively decreased. 

- Sporadic terror attacks targeted the Christian community, Christian leaders, 

and Christian facilities broke up, and now the attacks shifted to government 

officers, notably police officers. 

 

Poso conflict has taken 2000 people’s life, wounded 183,000 and caused 425,000 refugees, burned 

down 3,492 Muslim houses, three government offices, ten churches, and seven mosques. 

4.1.2 The Nature of Religious Conflict in Maluku 

The Maluku conflict occurred from 1999 to 2004 and broke up in Central Maluku (Ambon Conflicts) 

and the North Maluku conflict. Scholars have regarded the two conflicts as the worst communal 

conflicts after the New Order time as communal or collective actors dominated it. Terror attacks in 



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terms of bombing have become the strategy of attacks done during the conflicts. Maluku conflicts can 

also be phased into five, as shown in Table 2. 

 

Table 2. Phases of Maluku Conflict 

Phase Period Brief description 

1 1999/Ied 

Mubarak Day 

- The Ambonese hoodlums or gangsters from Jakarta arrived at Ambon 

- Muslim started to fight with Christian youth in Batumerah and Mahardika 

and then escalated to Haruku, Saparua, Ceram, Buru, Sanana, Manipa, 

Tanimbar and Tual.  

- Conflict between Kao Ethnic (Muslim) and Makian Ethnic (Christian) with 

support from Muslim Ethnic from outside Ternate broke up in North Maluku.  

2 June 

1999-April 

2000 

-Violence in Ambon broke up, Muslim militia burnt down Silo church. 

- Muslim attacked Christian in Tobelo, North Maluku. 

- North Maluku province was segregated from Maluku province.  

3 2000-2001 - Laskar Jihad and other paramilitary groups arrived at Maluku. 

- Republik Maluku Selatan(South Moluccas Republic/RMS)declared its 

secession agenda. 

- The government enacted Civilian Emergency Status (Darurat Sipil). 

4 2001-2002 - The government took strategic measures such as establishing integrated 

Batalyon to discontinue the conflict. 

- The conflicting factions reached the Malino Peace agreement. 

- Jafar Umar Thalib, Laskar Jihad leader, and Alex Manuputy, RMS leader, 

were arrested. 

5 2003-2004 - The conflict de-escalated. 

- The government revoked civilian Emergency in Maluku and North Maluku. 

 

Maluku conflict had taken 2,000 people in Central Maluku and 2,500 in North Maluku, caused more than 

250,000 as refugees, wounded 1,349 in Maluku and 2,004 in North Maluku. 

4.2 The Political Landscape in Poso and Maluku Conflicts 

4.2.1 The National Political Landscape  

Explaining social conflicts, including Maluku and Poso conflicts in the beginning reform in Indonesia, 

should discuss political dynamic at the national and local levels as, according to some political leaders 

and scholars, the nexus between them is clear. The contributing actors to the conflicts at its outset were 

allegedly from Cendana or Suharto cronies and elements from military police officers, which then used 

agent provocateurs. President Abdurrahman Wahid (Gus Dur) called the elements “the hand of Evil 

which created violence to ruin the nation and delegitimize government.” The Minister of Defense in Gus 



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Dur Administration, Juwono Sudarsono, explicitly pointed out that Suharto Cronies masterminded the 

conflict. They used Ambonese hoodlums to protect their interests (Aditjondro in Salampesy & Husain, 

2001) (Note 6). 

4.2.1.1 Political Conflict in the BJ Habibie Time 

Poso and Maluku’s conflicts broke up almost at the same time. They commenced in 1998-1999 though 

their de-escalation was somewhat different. These years were known as the beginning of reform, being 

marked by the step down of Suharto on May 21th 1998, and then succeeded by Baharuddin Jusuf Habibi 

(BJ Habibie), his former vice. As a former Suharto loyalist, Habibie had a dilemma on whether to provide 

full support to Suharto’s prosecution to fulfill reformist expectations or repay political favors he owed 

from Suharto during his former service with him. Habibie tried to play the game in a dilemma. He hired 

solicitor general Andi Ghalib to do a favor to Suharto. Ghalib stopped the allegation of corruption to 

Suharto, arguing that the evidence was insufficient (http. national. tempo, 2004) (Note 7). 

On top of that, he was not enthusiastic in hunting the grey status of the wealth of the Suharto family, nor 

did he take legal measures to clarify their legal status of corrupted items (http. Members. Tripod, 2018) 

(Note 8). As a result, Habibie’s reign was considered a weak government. During 15 

month-administration, he inherited the split of security forces and the conflict between the National Axis 

and the Habibie or Muslim Axis at the political and civil society level. Moreover, Habibie faced political 

maneuvers by Megawati’s so-called “rainbow nationalist groups,” which challenged his leadership. The 

group rallied in the streets to topple Habibi. In addition, the axis sponsored the establishment of student 

movements FORKOT and FARMED. Both the movements radically rallied in the street to demand his 

resignation. In addition to this, Habibie also lacked international support (Suaedy, 2000, Hasan, 2002; 

Simanjuntak, 2002) (Note 9).  

Habibie supporters formed the Habibie axis or Muslim axis to challenge political pressures maneuvered 

by the National Axis, comprising Islamic political parties and Islamic organizations. It also received 

support from “green generals or Muslim general who occupied structural position during Suharto’s last 

term (Suaedy, 2002; Hasan, 2002) (Note 10). Sponsored by high-rank police and military officers, 

Suharto family, and cronies, the Muslim axis established civilian security forces (Pengamanan 

Swakarsa/PAMSWAKARSA) to challenge FORKOT and FARMED (Note 11), whom they alleged as 

communists and deserve killing. On the contrary, the students’ movement accused the 

PAMSWAKARSA of pro-status quo (Aditjondro in Salampesy & Husain, 2001). (Note 12). The forces 

received training skill from the Army special forces (Komando Pasukan Khusus/Kopassus) 

(Simanjuntak, 2002) (Note 13). On top of that, the Suharto family also formed the other militias from 

nationalist backgrounds called Kelompok Merah (Red Group) (Note 14). 

4.2.1.2 Political Conflict in the Abdurrahman Wahid Time 

Through tough competition between the Nationalist and central axis groups, Abdurrahman Wahid (Gus 

Dur) took presidential office, succeeding BJ Habibie on 21 October 1999. Gus Dur also faced 

multi-layers political conflicts with different characteristics like his predecessor. While the political 



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conflict in Habibie’s time was sectarian, the conflict in Gus Dur Time was more political. Political 

pressure from the Nationalist axis withered after the step down of Habibie and the appointment of 

Megawati as the Vice President pairing with Gus Dur. 

This research classifies political conflict in Gus Dur Time into three; with the Suharto family, with the 

former supporter of Central Axis, and with military and police. The conflict between Gus Dur and the 

Suharto family had long occurred since Suharto was in power. Gus Dur, who served as an executive 

leader (Ketua Umum PB) of Nahdlatul Ulama, frequently criticized Suharto policy in defending the poor 

or marginalized people. Conversely, Suharto sought to topple Gus Dur from NU leadership and replace 

him with his man, yet unsuccessful. 

The conflict between Gus Dur and Central Axis started when political leaders of the Central axis were 

disappointed with a unique political maneuver of Gus Dur at the beginning of his administration. Gus 

Dur dissolved the Ministry of Social Affairs (Kementerian Sosial) and Ministry of Information 

(Kementerian Penerangan), arguing that in the regional autonomy, the function of the two Ministries 

belongs to the regional government. Gus Dur also replaced two cabinet members from the central axis; 

Jusuf Kalla of the Golkar Party and Hamzah Haz of PPP Parties. Because of this, leaders of the Central 

Axis accused Gus Dur of breaking their political contract. Gus Dur’s maneuver stimulated the anger of 

leaders of the Central Axis. This situation led to political instability until Gus Dur’s reign (Nasir, 2004) 

(Note 15). The nexus between the National political dynamics and Maluku conflict was evident when the 

anger of the leader of Central Axis to Gus Dur took the terms of supporting public sermon in Monas 

Square to wage national Jihad by defending their fellow Muslims in the Maluku conflict and demanded 

Gus Dur, whom they consider as weak, to stop the conflict. Otherwise, the sermon would demand DPR 

topple Gus Dur from the Presidential position. Furthermore, Gus Dur’s policy to solve Ambon was 

unacceptable when he delegated the responsibility to his vice, Megawati, and let the conflicting parties in 

Ambon solve their conflicts themselves (Suaedy, 2000) (Note 16).  

The conflict between Gus Dur and leaders of the military and Indonesian police began when Gus Dur 

sought to exercise objective and subjective control over the military and police by replacing the solid 

military and police leaders with their men. To implement his strategy, Gus Dur sacked high ranks army 

generals, using the allegation of TNI’s past human rights violations as a card to push the generals to leave 

their Power (Anwar, 2002; Nasir, 2004) Note 17). Unfortunately, Gus Dur’s strategy to put the military 

under control failed. TNI and Polri refused to obey his command. TNI perceived Gus Dur as having 

interfered them too far, uprooted him from TNI history, which positioned TNI, notably the army, as one 

of the pivotal political powers. Finally, Gus Dur’s trial to put TNI under civilian control was pointless 

(Nasir, 2004) (Note 18). The accusation worsened the conflict between Gus Dur and legislators to Gus 

Dur for swindling Bulog Money and Brunei Aid Money, generally called "Bulog Gate and Brunei Gate." 

The conflict ended with the impeachment of Gus Dur from the presidential position and replaced by his 

vice, Megawati, who enjoyed support from multi-political powers comprising from her own Party PDIP, 

former Gus Dur coalition of central Axis, TNI, and Polri. 



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The disappointed elements within the military used Laskar Jihad (LJ) as a “political bullet” to shoot Gus 

Dur. However, their deployment and service as a proxy military received no barriers from security 

officers and politicians, albeit rhetoric. Local Muslim paramilitary also warmly welcome the presence of 

LJ as it would strengthen their position (Hasan, 2008, Azca, 2004) (Note 19). The evidence of the 

influential role of TNI in masterminding the conflict in Maluku was the role of the retired one-star 

general Rustam Kastor, Ambonese Muslims, who confessed as LJ advisors. He stayed in Yogyakarta, a 

home base of LJ, monitored recruitment of LJ militia and supervised LJ training in Bukit Manjul Bogor 

prior to their deployment to Maluku (Kastor, interview 2011) (Note 20). 

4.2.2 The Local Political Landscape  

4.2.2.1 The Political Landscape in The Poso Conflict 

Important points to note in the previous discussion are the nexus between political conflicts in Jakarta, 

which produced agent provocateurs, and the political tension between multi-political powers and Wahid, 

which provide political context to the deployment of LJ in Maluku and Poso as well. The political rivalry 

along confessional lines happened prior to the Poso conflict. It extended from the rise of political Islam, 

pioneered by Ikatan Cendekiawan Muslim Indonesia (The Muslim Intellectual Association of Indonesia/ 

ICMI), at the national level. The sectarian politics fueled political competition between a Bungku 

Muslim candidate, Arif Patanga, who contested the regional head against Christian Pamona candidates 

Yahya Patiro and Drs Pelima in 1994-1995. Despite the tension, the result was acceptable as Patanga, 

who won the contest, accommodated Patiro as his secretary (Sangaji, 2007) (Note 21). 

This research classifies political conflicts amidst Poso religious conflict into two; first, conflicts between 

Muslim politicians and Christian politicians, supported by the respected leaders of their religious 

organizations. However, another conflict between a group of Muslim politicians followed the demise of 

the Arif Patanga administration, such as Abdul Muin Pusadan, Abdul Malik Syahadat, Damsyik 

Ladjalani, Akram Kamaruddin, Mas’ud Kasim, and Ismail Kasim, who competed for political positions 

against Christian politicians; Eddy F. Bangkudapu, Yahya Patio and former military officer Colonel 

Muljadi. Receiving strong backup from the Governor of Central Sulawesi, Pusadan triumphed the 

regional head of Poso. The governor was a former leader of HMI and closely linked with Islamic militant 

groups such as LJ. He also received covert support from former Golkar strongman, Habibie man, Arnold 

Baramuli (Damanik, 2003) (Note 22).  

Arif Patanga and Abdul Muin Pusadan shared same background. They hailed from the same ethnic group, 

Bungku, and served as ICMI local leaders. The problematic consequence of this primordial succession 

destroyed power-sharing with Christian leaders from Lori, Pamona, and Morias, prominent ethnic groups, 

who regarded themselves as being politically marginalized by the national political scenario sponsored 

by ICMI leaders. This situation led to conflicts as respected leaders of the conflicting groups hired agent 

provocateurs to provoke people for conflicts (Komnas, HAM, 2005, Agus, 2011; Aditjondro in 

Salampessy, 2001) (Note 23). In addition, the local religious leaders’ demands for the government 

worsened the tension. They demanded four measures: releasing Aghfar Patanga (Muslim Leaders) who 



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got detained for allegedly provoking people into conflict, replacing Yahya Patio (Christian figure) who 

occupied the position of secretary of regional head of Poso, with Damsyik Ladjalani and replacing 

Kapolres (Kepala Polisi Resort/Head of Regional Police) of Poso. Otherwise, they would burn one 

mosque and one church amidst the Patanga tribunal (Damanik, 2003) (Note 24).  

Likewise, Christian organizations like PGI echoed Christian victims’ defensive stance, especially when 

killed, but had a minimum role in discontinuing the conflict at the grassroots level. Muslim and Christian 

leaders blamed one–another and relied the quick solution of the conflicts fully on the government. After 

the Malino Peace agreement, they increased their trust in the government in maintaining peace in Poso, 

but the situation at the grassroots level was the other way around. In the view of human rights activists, 

the decreasing role of religious leaders in preventing the conflicts was to impress the national and 

international community that the Poso conflict was not a religious one (Agus, 2011) (Note 25).  

Second, the segregation of Poso into three regions, Poso, Morowali, and Tojo Una-Una, undoubtedly 

triggered the conflicts. The creation of the three regions stimulated Muslim discontent as it reduced them 

to a minority in the three segregated regions. However, it failed to improve people’s welfare as it only 

stimulated the competition of local Christian and Muslim politicians in occupying new political positions 

(Karnavian, 2008; Mashad & Yustiningrum, 2005) (Note 26).  

4.2.2.1. The Political Landscape in the Maluku Conflict 

This research theorizes the political landscape of the Maluku conflict into four internal political rivalries: 

first, the conflict between leaders of political parties and social organizations. Conflict in the political 

parties and social organizations occurred between Partai Demokrasi Indonesia Perjuangan (The 

Indonesian Democratic Party of Struggle/ PDIP), symbolized in red vis a vis Islamic political parties, and 

Golkar party, symbolized by white color. In Maluku, Christian figures who became strongmen of 

Christian militant groups dominated the structure of PDIP. In contrast, the pivotal figures from the 

Islamic community served as leaders of Islamic parties and Islamic organizations, such as Dewan 

Dakwah Islamiyah Indonesia (the Indonesian Islamic Preaching Council/DDII), Majelis Ulama 

Indonesia (The Indonesian Clerics Council/MUI), Muhammadiyah, and the Masjid Al Fatah Foundation. 

However, the leaders failed to halt the escalation of the fightings between Muslims and Christians in 

Ambon spilled over by the gangsters from Ketapang, Jakarta (Hasan, 2008; Van Klinken, 2007; Suaedy, 

2000) (Note 27).  

At the operational level, the interest of the Muslim group, as previously discussed, was effectively 

echoed by a retired one-star general, Rustam Kastor. The negative perception between Christian leaders 

and Muslim leaders intensified the conflict. Christian leaders regarded the conflict as “a big national 

plot” targeted at destroying Maluku as the national center of Christianity in the eastern part of Indonesia 

(Papilaya in Kleden & Julaman, 2000) (Note 28). Christian leaders also pointed out additional supporting 

facts triggering the conflict, namely segregating Gorontalo from Manado, segregating North Maluku 

from Maluku, the migration of non-Christian inhabitants to eastern areas of Indonesia aiming at 

accommodating Muslim community (Salam) and improving their economic life in Gorontalo and North 



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Maluku. At the same time, it would weaken the Power of Molluscan Christians (Serani), who, as they felt, 

as the most educated Christians in Indonesia. This scenario became a trial project before being developed 

in other parts of Indonesia.  

On the contrary Muslim leaders, as voiced by Rustam Kastor, reject the accusations that the Maluku 

conflict was rooted in the economic disparity between Bugis Buton Makasar (BBM) ethnics and native 

Christians and the transformation of bureaucracy which sidelined Christians. Instead, it was rooted in the 

movement of the secessionist group of Republik Maluku Selatan (The South Maluku Republic/ RMS), 

which Christian activists dominated. Allegedly receiving support from the United States of America 

(USA), this group sought to separate Maluku from Indonesia, while other Christian groups sought to 

purge the Muslim community from Maluku (Papilaya in Kleden & Julaman 2000) (Note 29). In addition, 

the US was suspiciously planning Maluku Island as its Military base that would replace its base in the 

Philippines. The US-backed RMS, which later cooperated to develop its military base (Kastor, Interview, 

2011) (Note. 30). 

During this time, rumors that Megawati of PDIP supported Christian groups and Habibie, the leader of 

Golkar and ICMI, supported Muslim groups circulated in the militant grassroots groups (Hasan, 2002) 

(Note 31). As a result, Golkar activists attacked the house of PDIP leader John Maliola, where PDIP 

activists commemorated the attack of the Jakarta PDIP office in July 1997. Many speculated that the 

reason behind the attack was the frustration of Golkar politicians for losing the party influence against 

PDIP, which controlled 53% of electoral votes in Maluku (Van Klinken, 2007) (Note 32). 

Second, the conflict between social and political leaders in Maluku, which suspiciously received support 

from national political elites, erupted along with the conflict between government leaders Governor 

Saleh Latuconsina and the regional military commander over the implementation of President Gus Dur 

instruction to enact civilian emergency status. The governor complained over the insubordination of 

military commanders to the governor, who assumed full responsibility for implementing civilian 

emergency status. The conflict between the governor and provincial military commander escalated 

amidst the tension between Muslim and Christian bureaucrats in the local government (Manuputi & 

Watimena in Trijono, 2004) (Note 33). The rise of ICMI during the last term of Suharto’s tenure, which 

resumed to reform time, provided powerful support to Muslim bureaucrats to take over the leadership 

position of Christian bureaucrats, who had been for decades, dominating the leadership. The transfer of 

domination also received support from Muslim governors and ICMI backgrounds. Political tension 

flared when Christian bureaucrats defended their position in Ambon Mayor and Pattimura University 

(Bertrand, 2004) (Note 34).  

Third, the conflict at the bureaucratic level took its seeds in the leadership rivalries in the student 

organization at Pattimura University. Muslim students organization such as Himpunan Mahasiswa 

Indonesia (Islamic Student Association/HMI), Persatuan Mahasiswa Islam Indonesia (Islamic Student 

Union of Indonesia/PMII), Ikatan Mahasiswa Muhammadiyah (Muhammadiyah Student 

Association/IMM) worked together to challenge the Nationalist and Christian student universities, 



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Gerakan Mahasiswa Nasionalis Indonesia (The Nationalist Student Movement/ GMNI) and Persatuan 

Mahasiswa Kristen Republik Indonesia (Christiant Student Union /PMKRI). Allegedly benefiting from 

the corruption, collusion, and nepotism (KKN) practices of Christian university administrators in favor 

of them, GMNI and PMKRI leaders took control over students unions on the campus. As a result, 

Muslim student leaders felt marginalized or mistreated, despite their proven competencies (Ex 

Combatant, Interview, 2011) (Note 35). Unfortunately, because of poor strategy, Muslim organizations 

such as Badan Imarah Muslim Maluku (BIMM) did not provide sufficient support to the development of 

the career of Maluku Muslim youths (Kastor, Interview, 2011) (Note 36). 

Forth, before the conflict, there was a shift of domination in the organization’s leadership structure from 

Christian Mollucan activists to Muslim Mollucan activists with HMI-MPO background, which also 

affiliated with Golkar. This rivalry served as an extension from the rivalry in the student union in 

Pattimura University and preceded the shift of domination from the Golkar Party, which was influential 

in the New Order time, to PDIP as the new leading political power in the Reform time. The domination of 

HMI-MPO in the KNPI leadership triggered the exodus of KNPI activists with nationalist and Christian 

backgrounds from the Golkar Party to PDIP (Ex Combatant, Interview 2011) (Note 37). Out of conflict 

in Central Maluku, the conflict also broke out in North Maluku (Van Klinken, 2007) (Note 38). Conflict 

in North Maluku was rooted in two political causes. First, the Christian minority refused the segregation 

of North Maluku to the New District of Malifut, whose majority population was Muslims. The Christians 

were worried that they would lose control over the new regions implicated in the difficulty in the 

evangelization project as it would receive full backup from political Islam sponsored by ICMI (Bertrand, 

2004) (Note 39). 

On the contrary, North Maluku Muslims accused Christians would build the new region as the most 

influential center of evangelization in the region (Ex Combatant, Interview 2011) (Note 40). Second, the 

competition between Sultan of Ternate and Sultan of Tidore to win the governor position in the new 

province of North Maluku. The former relied on Christian inhabitants in North Halmahera, while the 

latter got support from Makianese Muslim inhabitants in central and south Halmahera. On top of that, the 

two Sultans also competed to control the influence over Australian gold mining projects in Halmahera. 

 

5. Conclusion 

Indonesia is a pluralistic country where diverse ethnicities, tribal groups, and religious adherents live in 

peace and harmony. However, Indonesia also experiences conflicts, violence, terrorism, and tensions 

amongst religious followers. This research is about the dark dots of Indonesian history. It seeks to 

analyze similarities and differences of conflicts intertwined with terrorism in Maluku and Poso in two 

things: the nature of the conflicts and terrorism and political dynamics explaining the conflicts. This 

article uses two concepts, religious conflict and the landscape of political conflict, as frameworks to 

analyze the collected data. It borrows the concept of religious conflict developed by Horowitz and 

Tadjudin, who look at conflicts from their negative perspective regarding attacking and injuring between 



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two-religious followers. While analyzing the nexus between political and religious conflicts, this article 

combines theoretical frameworks developed by Samuel Huntington (1991), Jack Snyder (2003), O’ 

Donel, and Phillip Schmitters. They have long alerted that conflicts, violence, and revolution have 

become a harmful by-product of initial political democratization. 

This research used a comparative method with collecting data from documents, news, and interviews and 

concluded that Poso and Maluku conflicts share similarities and differences. First, they broke up in stages 

of escalation. Second, the government has initiated a peace agreement called the Malino agreement to 

solve the conflicts. In the Maluku conflict, the Malino agreement relatively de-escalated the conflict. In 

the Poso conflict, the Malino agreement shifted the conflict from communal to asymmetric or terrorism, 

even until today. 

This research also finds similarities and differences. They were similar in that both conflicts happened 

amidst the national political conflicts during Habibie and Abdurrahman Wahid’s time and de-escalated in 

the Megawati Time. The residuals of Suharto’s past misconduct burdened Habibie’s reign, the split 

between Muslim Axis associated with him versus the nationalist axis associated with Megawati. The 

presence of ICMI and Golkar institutionalized Islamic politics. 

The two-year Wahid reign was dynamic and tense as Wahied conflicted with the Suharto Family, Central 

Axis, his former supporters of and with military and police. Conflict with the Suharto family extended 

their previous conflict during the New Order Era. The conflict with Central Axis has resulted in the 

disappointment of its leaders with Wahid’s unique political maneuver. In contrast, conflict with military 

and Polri leaders was rooted in Wahid’s intention to exercise subjective and objective control over the 

security institutions by replacing their leaders who were not of his preference. The local political 

landscape explaining Maluku and Poso conflicts also shares similarities and differences. They are similar 

in the following; first, they experienced conflicts between Muslim political and social leaders. Political 

leaders in the two conflicting regions competed for political and bureaucratic positions. Muslim political 

leaders received back up from ICMI and benefited from Golkar’s influence. Second, regional segregation, 

later known as regional autonomy, also contributed to the conflict. 

This research also finds differences in the political explanations. First, while the conflict between 

Muslim political leaders and Christian political leaders in Poso circulated in Golkar Party with the 

support of leaders of Islamic parties, political conflict in Maluku took place between Muslim politicians 

with ICMI and Golkar background vis a vis Christian politicians associated with PDIP. Second, conflicts 

between leaders of Muslim and Christian student organizations and bureaucrats to win leadership in 

Patimura University triggered political conflict in Maluku and continued the rivalry between Muslim and 

Christian youth leaders to occupy KNPI leadership. In contrast, such conflict was not present in Poso 

religious conflicts. 

 

 

 



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Note 1. 

https://www.bbc.com/indonesia/berita_indonesia/2016/02/160218_indonesia_radikalisme_anak_muda. 

accessed 25 August 2018 and Adje Suraji, Ancaman Radikalisme https://nasional.kompas.com/read 

/2016/11/24/08520891/ancaman.radikalisme. Accessed 25 August 2018. 

Note 2. Panggabean 2004, “Approach to Ethnic and Religious Conflict Resolution,” in Lambang 

Trijono, eds., The Making of Ethnic and Religious Conflict in South East Asia: Cases and Resolutions, 

Yogyakarta: CSPS Books, pp. 56-57. 

Note 3. Sukma 2005, Ethnic Conflict in Indonesia: Causes and the Quest for Solution, In Snitwongse, 

Kusuma & Thompson, W. Scott, Eds., Ethnic conflict in Southeast Asia (Singapore: ISEAS,2005), 

pp.1-41, Trijono 2004, Ibid.p.4. 

Note 4. Tadjoeddin 2013, “Educated but Poor: Explaining Localized Ethnic Violence During 

Indonesia’s Democratic Transition,” International Area Studies Review, Vol. 16, no. 21, pp. 24-49. 

Note 5. In the Malino Peace Agreement 1, the warring Muslims and Christians came to a consensus on 

ten articles: stopping the conflict, enforcing law and order, rejecting foreign intervention and civilian 

emergency status, respecting one another mutually, stopping betrayal, and letting victims of the conflict 

come back to Poso, returning all belongings and properties to their owners, helping IDPs to return to 

their homes, promoting tolerance to Muslim, Christian and other religious adherence in practicing their 

faith, working hand in hand with the government in the recovery and rehabilitation programs 

(www.upi.edu. 2009). 

Note 6. Aditjondro 2001, “Di balik Asap Mesiu, Airt mata dan Banjir Darah di Maluku,” in Zahirin 

Salampessy & Husain (Eds.), Ketika semerbak Cengkih tergusur Asap Mesiu. Jakarta: TAPAK Ambon, 

pp. 147-154. 

Note 7. Nasional Tempo, 25 Maret, 2004, 

https://nasional.tempo.co/read/41026/soeharto-koruptor-terkaya-di-dunia, accessed, 25 August, 2018. 

Note 8. http://members.tripod.com/kkn_ghalib/galibtempo1.htm, accessed 25 August 2018. 

Note 9. Suaedy, et.al 2000, Luka Maluku: Militer Terlibat, Jakarta: Institut Studi Arus Informasi, 

pp.48-51. Hasan, 2002 “Faith and Politics: The Rise of the Laskar Jihad in the Era of Transition in 

Indonesia”, Indonesia, vol. 73, pp. 160-164. Simanjuntak, 2002, Premanisme Politik (Jakarta: Institut 

Studi Arus Informasi, p. 62. 

Note 10. Suaedy. Ibid. Hasan, Ibid  

Note 11. FORKOT stands for Forum Kota (city forum) while FAMRED stands for Forum Aksi 

MahasiswaUntuk Reformasi danDemokrasi (Forum of Student Action for Reform and Democracy). 

Both were radical nationalist student movements, which arose in the early years of reformasi. Their 



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pragmatic mission demanded Habibie’s resignation from the presidential office, arguing that Habibi 

was the leader foremost in defending the status quo of Suharto’s era. 

Note 12. Aditjondro. Op Cit.  

Note 13. Simanjuntak, 2002, Op. Cit. 

Note 14. Militia groups which had close connections with the Suharto familiy were Satgas Tebas and 

Laskar Putih. Members of the Nationalist Militia “red group” were Satgas Wirapati, Satgas Samber 

nyawa, Pasukan Banteng Tengkorak, Satgas Pasopati, Dewaruci (whose members are 66 retired Navy 

force), Pasukan Bela Mega and other militias who joined PDIP, numbering50-thousands (Simanjuntak, 

PremanismePolitik), pp. 60-62. 

Note 15. Nasir, 2004, Konflik Presiden Versus Polri di Era Transisi Demokrasi, Jakarta: Pusat Studi 

Politik Madani Institute, pp. 142-143. 

Note 16. Suaedy. Op.Cit.  

Note 17. The long lists allegation of past Human Rights Violation were: the massacre of civilians in 

Santa Cruz, East Timor, the assassination of the labor activist Marsinah in East Java, the assassination 

of a journalist in Jakarta, the homicide of protesters demonstrating against the construction of the 

Kedung Ombo and Nipah dams, the killing of Muslim activists in Tanjung Priok, North Jakarta, the 

heinous military operations against the Aceh Liberation Movement (GAM: Gerakan Aceh Merdeka) 

fighters, and the abduction of student activists during the later years of the New Order regime (Anwar, 

2002, Wahied Versus Militer: StudiTentangHubungan Sipil-Militer di Era Transisi, Jakarta: Grasindo) 

Nasir, 2004. Op. Cit.  

Note 18. Nasir 2004. Ibid.  

Note 19. Hasan. Op. Cit. Azca, 2004. Security Sector Reform, Democratic Transition, and Social 

Violence: The Case of Ambon, Indonesia: Berghof Research Center for Constructive Conflict 

Management, pp. 444-445. 

Note 20. Interview With Brigadier General TNI (retired) Rustam Kastor, ex Commander of Korem 

XVII/Trikora, Advisor of Laskar Jihad, in Ambon, 2 April 2011. 

Note 21. Sangaji 2007, Aparat Keamanan dan Kekerasan Regional Poso,in Henk Schulte Nordholt & 

Gerry van Klinken, eds., Politik Lokal di Indonesia: Jakarta: Yayasan Obor Indonesia, p.5. 

Note 22. Damanik. Op.Cit. 

Note 23. Komnas HAM. Op. Cit. Agus. Op. Cit and Aditjondro. Op. Cit. 

Note 24. Damanik. Op. Cit. 

Note 25. Agus. Op. Cit.  

Note 26. Karnavian, 2008, Indonesian Top Secret: Membongkar Konflik Poso; Jakarta: PT Gramedia 

Pustaka Utama. pp. 374-375, Mashad and Yustiningrum, 2005. Negara dan Masyarakat dalam Resolusi 

Konflik Poso, in Syafuan Rozi, Resolusi Konflik di Ambon dalam Hubungan Negara dan Masyaraka 

tdalam Resolus iKonflik di Indonesia, Kasus Sulawesi Tengah, Maluku, dan Maluku Utara: Jakarta: 

LIPI. pp. 45-88. 



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Note 27. Hasan. Op. Cit, Van Klinken. Op. Cit and Suaedy, Op.Cit 

Note 28. Papilaya, 2000, Persepsi Lokal tentang Konflik dan Kekerasan di Ambon- Persepsi Protestan, 

in Ignas Kleden &John Julaman, eds., Laporan Seminar: Timur dan Barat di Indonesia, Perspektif 

Integrasi Baru. Jakarta: The Go-East Institute pp. 50-52. 

Note 29. Papaya. Ibid. 

Note 30. Kastor, Interview. Op. Cit. 

Note 31. Hasan. Op. Cit. 

Note 32. Van Klinken. Op.Cit 

Note 33. Manuputi and Watimena, 2004, Konflik Maluku, in LambangTrijono., et al., Potret Retak 

Nusantara: Studi Kasus Konflik di Indonesia, Yogyakarta: CSPS, pp. 147-148 

Note 34. Bertrand, 2004, Nationalism and Ethnic Conflict in Indonesia, Cambridge: Cambridge 

University Press, pp. 118-119. 

Note 35. Interview with Combatant in North Maluku, Interview, 20 December 2011. 

Note 36. Interview with Kastor, Op. Cit. 

Note 37. Interview with Ex Combatant. Op. Cit.  

Note 38. Van Klinken. Op. Cit. 

Note 39. Bertrand. Op. Cit. 

Note 40. Interview with ex-Combatant.Op.Cit. 

 


