Focusing on Southern Thailand and Mindanao, this article critically examines the way in which the governments’ response is affecting and transforming the role of local religious leaders in these conflicts. The perception of religion, Islam in particular, is complicating mediation efforts and preventing governments from designing feasible conflict resolution policies that seek to accommodate reasonably legitimate aspirations. Michael Vatikiotis traces the culturally and ethnically motivated struggle for independence in the region and illuminates how it is increasingly drawing on religion as a motivational tool.