This article examines the roles of religion in the contemporary separatist movement in southern Thailand, whose violent campaigns have dramatically surged since 2004. It locates Islam in the regionâ€™s own political and historical context rather than viewing it as an expression of transnational terrorism or casting Islam as of secondary importance in what is seen as primarily an ethno-nationalist struggle, as some scholars have done. I argue that Islam served as a powerful motivational frame that drove thousands of Malay Muslims to take part in the violent struggle led by the Patani Malay National Revolutionary Front (BRN), as a sacred justification for their violent actions and as a blueprint of a new socio-political order. The conflict was elevated into a cosmological battle and the fightersâ€™ actions were fundamentally framed within Islamic theology. Islamic law was employed as a primary reference for the justification and regulation of violent attacks. This article also demonstrates that Islam is part of the BRNâ€™s political agenda and fighters have turned their perceived Islamic beliefs and norms into military actions. However, its ideological orientation is at variance with that of the transnational jihadists. This article offers a more nuanced approach to understanding the religious dimensions of this conflict.