Purpose: The violent conflict in Ambon, Indonesia (1999-2002) - which claimed more than 2,000 lives - occurred when a dominant ethnic group (Ambonese) was challenged by new ethnic groups (non-Ambonese: Bugis, Butonese, and Makassarese). The conflict intensified and evolved into a religious one between the Christians (mostly Ambonese) and the Moslems, consisting of Ambonese and the non-Ambonese. The absence of a long-term societal re-integration strategy that emphasized on the management of group diversities had resulted in a pseudo or fragile integration that led to societal disintegration. Following the regime change in 1998, a violent communal conflict or "politics by other means" occurred since the conduciveness of the local situation was related to national politics. Method: Using Ambon as a Case Study, the chapter analyzes the trajectory of the conflict and its resolution. Findings: The conflict grew more extensive ever since the failure of the state, particularly the police and the military that became partisans in order to protect their families or to benefit from security businesses. The peace building efforts took in several stages involving various social organizations as well as governments at the local and the national level. These processes were facilitated by general election or "war by other means" that transformed the violent conflicts to non-violent competition or from bullet to ballot.