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The recent surge of violence and intolerance against religious minority communities, both Muslim and non-Muslim, in Indonesia during the process of democratic consolidation has raised a broader issue in regards to religious freedom, minority rights, and relations between faith communities in emerging multi-religious democracies. Why are religious minorities at times perceived as a threat to peaceful inter-religious relations and national stability, despite their vulnerable position? Under what conditions – and how – is the perception of threat translated into collective violence? This paper will look into post-independence regime policies towards religion to suggest that the threat perception among Muslim religious elites changes over time depending on the regime formation; that is, the Muslim elites’ quest for – and consolidation of – state power. Based on original empirical data, interviews and historical accounts, I will historically trace the perceptions, attitudes, and strategies among Muslim religious elites towards other communities and elites to demonstrate that anti-minority mass mobilization is primarily the result of political and religious elites’ quests for power in order to secure their survival in the face of a perceived threat to their institutional power and authority. My findings repudiate the structuralist’s proposition of “secularization” and “Islamization” and the primordialist’s claim about an “ancient hatred” between – and among – faith communities and sectarian difference; instead, I conclude that religious freedom and tolerance (or a lack thereof) is largely conditioned by political competition among secular and religious elites within the majority Muslim community.