In January 1999, sudden and surprising violence broke out between Christians and Muslims in Indonesia's province of Maluku. Previously seen as a stable region in the archipelago, it quickly became the site of devastating inter-religious strife. Thousands of people were killed in a spiral of violence over the following years. Little known in the rest of Indonesia and mainly neglected under the Suharto regime, Maluku became a core preoccupation of the Habibie, Wahid, and Megawati governments.

The conflict was a consequence of New Order policies that disrupted the balance of forces between the two communities. One of the few regions where both religious groups were almost equal in number, Maluku was the site of a silent, fragile competition for power between Christians and Muslims. Patrimonial networks reinforced group identities, as powerful and lucrative positions in the civil service became major sources of resources and protection for each religious community. Under the New Order, access to such networks represented one of the few channels through which groups could advance their interests.

The Islamization of the Suharto regime in the 1990s disrupted the fragile balance in Maluku. Muslims gained a new sense of confidence to challenge the longstanding Christian dominance. Christians concomitantly felt threatened. With a growing fear that the government was becoming Islamized, they were worried about losing the positions of power that ensured the security of their community.