Religious identities and institutions present significant challenges in contemporary Indonesia as they are linked to understandings of social cohesion, security, and national identity. Today, debates around religion center on understandings of security threats (including both extremist tendencies and public order and morality), and on respective responsibilities of the central government versus local authorities for oversight and regulation of religious matters. This brief highlights both historical and contemporary religious factors that threaten harmony and progress on human rights in Indonesia. WFDD Executive Director Katherine Marshall was a lead author on the brief, developed as part of the Southeast Asia: Advancing Inter-Religious dialogue and Freedom of Religion or Belief project.