This article discusses the idea of 'Southern theory', which is presented as both decolonized and autonomous social science. The article first discusses the idea of the 'South' as a heuristic concept, suggesting that it is more a metaphor or a symbol of intellectual subalternity. This leads to a specific understanding of the meaning of Southern theory as decolonial social science. I then discusses the idea of the decoloniality of the social sciences and present some traits of the social sciences in the decolonial mode of knowledge production. Seven features of decolonial social sciences are listed. The article also discusses examples of doing decolonial social sciences, specifically the demystification of mainstream discourse, and knowledge production that serves democratic ends and which is not unconnected its social milieu. The cases of Islamic economics, the persecution of Shi'ites in Malaysia, and Hindu-Muslim relations in Malaysia are discussed. The article ends with a brief discussion on the understanding of Southern theory, or knowledge in the mode of decoloniality as autonomous social sciences. They draw upon both Western social sciences as well as the various local knowledge traditions of the South. Autonomous social sciences are defined as autonomous from both Orientalist/Eurocentric discourse as well as narrow state, nationalist and sectarian agenda.