After more than a decade studying the Indonisian pesantren the author had an opportunity to visit similar institusions in Thailand. After placing them in historical context this paper explores how these institutions vary in Southeast Asia. Although it is reasonable to presume that pondok betwen different countries and aras in the region started out virtually indistinguishable in form and function local and national histories have shaped them diferently. This paper explicitly compares pondok in three distinct areas Indonesia Nakhon Sri Thammarat and the Deep South in Thailand the former two based on fieldwork and the latter based on literature review. It is common for some analysts and governments to associate pondok with violence. The evidence suggests that this is misplaced. The paper concludes that before an authoritative statement can be made on this point more research is needed.