Transgendered Indonesians live in the fourth most populated nation in the world with more Muslims than any other country. This thesis summarizes an ethnography conducted on one religiously oriented male-to-female transgender community known in the city of Yogyakarta as the waria. This study analyzes the waria’s gender and religious identities from an emic and etic perspective, focusing on how individuals comport themselves inside the world’s first transgender mosque-like institution called a pesantren waria. The waria take their name from the Indonesian words wanita (woman) and pria (man). I will chart how this male-to-female population create spaces of spiritual belonging and physical security within a territory that has experienced geo-religio-political insecurity: natural disasters, fundamentalist movements, and toppling dictatorships. This work illuminates how the waria see themselves as biologically male, not men. Anatomy is not what gives the waria their gender, their feminine expression and sexual attraction does. Although the waria self-identity as women/waria, in a religious context they perform as men, not women.