The Maluku Islands sectarian conflict was a period of ethno-political conflict along religious lines, which spanned the Indonesian islands that compose the Maluku archipelago, with particularly serious disturbances in Ambon and Halmahera Islands. The duration of the conflict is generally dated from the start of the Reformasi era in early 1999 to the signing of the Malino II Accord on 13 February 2002.
The principal causes of the conflict are attributed to general political and economic instability in Indonesia following the fall of Suharto and the devaluation of the rupiah during and after a wider economic crisis in Southeast Asia. The forthcoming division of the then Maluku province into the current Maluku province and North Maluku province exacerbated existing district political disputes further and, as the political dispute had been characterized along religious lines, inter-communal fighting broke out between Christian and Muslim communities in January 1999, cascading into what could be described as all out warfare and atrocities against the civilian population committed by both sides. The main belligerents were therefore religious militia from both faiths, including the well organised Islamist Laskar Jihad, and Indonesian government military forces.
Though all violence during the four-year period cannot be linked directly to political or sectarian issues, as a significant majority could be attributed to opportunistic crimes, the violence was categorized by the armed campaigns of local militia groups targeted almost exclusively against the civilian populations of the islands. This also included the Laskar Jihad militia group, composed of trained fighters from other predominantly Muslim areas of Indonesia, who ran a campaign in the later stages of the conflict to drive out Christian residents of Maluku. The nature of the violence was intended to displace members of the rival community, as it assumed the form of mass-evictions through the use of intimidation and harassment, followed by vicious attacks on large groups of locals and arson attacks on their residences or even whole neighbourhoods that could be termed as pogroms in some cases. In one instance in April 1999 all Christian residents were expelled from the Banda Islands.