State recognition of religion and religious laws potentially has far-reaching implications for human rights and racial justice, not all of which will have been intended or even anticipated. The paper seeks to examine the impacts of state recognition of religion, or the state privileging religion(s) and the attempt to forge national identity on racial injustice. It argues that wherever State authority(ties) attempt to enforce religious ‘unity’ certain racial minority groups are perceived as ‘politically subversive’ and therefore excluded from mainstream society. This always leads to intolerance of differences, racial discrimination, and violations of human rights. This paper addresses the questions of what the religious landscape in ASEAN/SEA looks like; what is the relation between religious identity and conceptions of nationhood/national identity; have countries in ASEAN/SEA experienced religion-related social/racial hostilities; how tensions are manifested; and how is it that religions—which supposedly espouse peace, love, and harmony—are so commonly connected with intolerance, conflicts, and discrimination. Based mainly on the literature review, the paper unpacks the questions individually. It also provides evidence on the ground through analyzing the cases of Singapore and Thailand. The paper concludes that the fact that a particular religion is privileged, or a certain ‘identity’ or ‘social harmony’ is required or imposed to become full members of any political community, it tends to create conditions for intolerance and discrimination and racial injustice.