Tensions between the Muslim and Christian communities rose gradually in the decades since the 1950’s to the point where small differences could easily set off violence. The Asian financial crisis of 1997 effected morale and led to the inevitable desire for scapegoats. The fall of Suharto in May 1998 was accompanied by calls for redress of injustices and other inflammatory rhetoric. Furthermore, since the authorities were unable to calm low-level incidents, a cycle of revenge began, with vigilante justice and vilification of entire groups.
For Maluku, the first major event came between February and April 1998, when the Malukan Muslim leader in Jakarta, Deddy Hamdan, disappeared along with other pro-democracy activists. The elite force of the Indonesian army, Kopassus, was implicated in the kidnapping. Deddy Hamdan was replaced as leader of the Malukan Muslim Youth by Ongen Sangaji, a member of Pemuda Pancasila, an organization which included many violent ex-criminals who had supported Golkar and had been accused of violent attacks throughout Indonesia against perceived enemies, including moderate Muslims.
On 22 November 1998, a gang fight took place in Jakarta’s Ketapang district between Ambonese Christians and Muslims. Rumors spread that Ambonese Christians had burnt a local mosque, leading to a rampage of killing and church-burning. Many of those involved were trucked in from elsewhere, leading to speculation that “provocateurs” were involved.

The catalyst, January 1999

The explosion of sectarian violence in Maluku occurred in Ambon on 19 January 1999 with a dispute between a Christian bus driver and two Muslim passengers. This dispute occurred at a tense time because of the advent of the Muslim holiday of Id-al-Fatr, a prominent time for prayer and ceremony. Local residents had already begun arming themselves against possible attacks. Within hours of the incident, fighting had spread throughout the city, with violent mobs from both sides attacking neighborhoods.
The fighting spread almost immediately to the nearby islands of Haruku, Saparua, Seram, and Manipa. Muslims from Sulawesi and Ambonese Christian gangsters from Jakarta were allegedly also involved. For the first month of the violence, most of the deaths were caused by traditional or homemade weapons, or by house-burnings. From mid-February, government security forces received orders to shoot troublemakers on sight. They carried out their orders indiscriminately, using live ammunition and firing into crowds – acts that resulted in hundreds of civilian casualties.
The next wave of violence came in July 1999, in the area of Ambon City, where refugee camps sheltering the displaced on both sides of earlier fighting were located. A rock-throwing incident between Christian and Moslem youths on 27 July led to riots in Ambon City and widespread destruction of property.
In August 1999, the conflict spread to North Maluku. As it was now becoming a separate province, the Makianese who controlled the Ternate bureaucracy wanted to create a new administrative district centered on Malifut, a nearby town which would allow the Makianese to take over from the Kao villages a gold mine which was the main local source of revenue. At the moment of the inauguration of the new district fighting broke out between Malifut residents and those of a Kao village. Convinced by the Ternate sultan , the Kao laid down their arms; however, hatred ran high, and in October, the Kao destroyed Malifut, killing 100 of its inhabitants, and forcing the 4000 survivors to flee to Ternate and the neighboring island of Tidore.
The Makian-Kao conflict began as an ethnic rather than religious conflict, demonstrated by the loyaty of the Christian Kao to their Muslim sultan. However, the Muslim flight to Ternate and Tidore was accompanied by a rise in religious hatred and the Makians “cleansed” Ternate of Christians. The Ternate sultan refused to support the violence, so they turned to the sultan of Tidore, a traditional rival of Ternate. Due to his support of Christians, the sultan of Ternate was quickly labeled as anti-Islam and was his police forces were beaten. Currently, supporters of the sultan of Ternate and other supporters of Christians are afraid to speak out, thus their political influence has since been marginalized.
Fighting raged throughout the latter part of 1999, reaching a peak in December, with the military and police allegedly taking part in the killing. Another traffic incident involving a Christian and a Muslim on 26 December 1999 led to the worst rioting in a year, including the burning of Silo church, the largest protestant church in the region. In the Tobelo District on Halmahera island, north of the Kao area, Christians attacked the local Muslim minority, killing 500 and “cleansing” the district of over 10,000 survivors. In turn, this strife led to Muslim calls for jihad to get their land back and to “cleanse” the area of Christians.
In mid-2000, two thousand members of the Java-based militant Islamic group, Laskar Jihad, led by Jaffar Umar Thalib, arrived in Maluku, tipping the balance of power in favor of the Muslim factions. The influx of additional fighters led to increased violence around Ambon. Since 1999, it is estimated that 5,000 people have been killed and 500,000 displaced as a result of the conflict.

Likelihood of continuation

The violence has undermined local trust both in political institutions and the rule of law. The army may now indeed be in a stronger position in public opinion, as the only body that can protect people - even if evidence supports accusations of playing a role in the violence. Meanwhile, throughout Indonesia, Christian-Muslim relations have been eroded by these events, leading to the possibility of further violence elsewhere. NGO workers estimate that forgiveness among the Maluku survivors will come slowly, and that reconciliation will take at least five or six years.
In February 2002, Christian and Muslim factions signed a peace accord in Malino, Sulawesi. Laskar Jihad, the militant Islamic group cited by many as fueling conflict in Maluku, refused to attend the Malino talks. The Malino Peace Accord calls for the disarming of all militias, and the creation of joint security patrols, and establishes a framework for the return and resettlement of refugees. It remains to be seen whether the agreement will lead to lasting peace. The explosion of two bombs in Ambon only one day after the Accord was signed has contributed to uncertainty about the long-term prospects for peace in Maluku.