Maluku Sectarian Conflict (1999 to 2002)

This article records tradition as it has been passed down and reported. Its sources are not yet part of the atlas's verified catalogue.

Communal fighting between Christian and Muslim militias swept across the Maluku islands of eastern Indonesia beginning with a street clash in Ambon on 19 January 1999, escalating over the following three years into organized sectarian warfare. Each side raised armed militias, most prominently the Java-based Laskar Jihad, which arrived by the thousands from 2000 to fight on the Muslim side. The violence broke out amid the political instability that followed the 1998 fall of President Suharto's government, in a province where decades of state sponsored migration and civil service and military patronage had already strained the earlier rough parity between the islands' Christian and Muslim populations.

Fighting displaced hundreds of thousands of people and divided towns and neighborhoods along religious lines before the Indonesian government brokered the Malino II Accord, signed by representatives of both communities on 12 February 2002. The accord formally ended the organized fighting, though sporadic violence continued for several years afterward, and it left Ambon and other Maluku towns religiously resegregated in ways that persisted long after the peace agreement. Several militia figures were later prosecuted for their role in the violence, though Indonesia's courts reached only a small number of the participants on either side.

This article records tradition as it has been passed down and reported. Its sources are not yet part of the atlas's verified catalogue.

The International Crisis Group's own February 2002 assessment, published days before the Malino II Accord, put the Maluku conflict's toll at a minimum of five thousand and as many as ten thousand deaths across the three years of fighting, a range Gerry van Klinken's academic study of Indonesia's communal violence during the same period treats as the best available estimate rather than narrowing it further. No single reconciled count has superseded that range, so this atlas records it as the Crisis Group itself gave it rather than adopting either bound as final.

Van Klinken's study reads the conflict's roots as substantially local and political rather than doctrinal: competition over civil service positions, migration policy and control of local government, tensions that predated the fighting and outlasted the religious language later layered onto it. The fighting nonetheless divided combatants and, increasingly as it continued, entire neighborhoods and towns along Christian and Muslim lines, and the arrival of the explicitly jihadist Laskar Jihad militia from 2000 gave the conflict's later phase an overtly religious framing it had not fully carried at the outset. The Indonesian military and police were present throughout and were repeatedly accused by both sides of favoritism, a further complication no single account of the conflict's causes fully resolves.