The attempt to expand the discourse of science and religion by considering the pluralistic landscape of today’s world requires not only adding new voices from more religious traditions but a rethinking of the basic categories of the discourse, that is, “science,” “religion,” and the notion that the main issue to be investigated is the relationship between the two. Making use of historical studies of science and religion discourse and a case study from Indonesia, this article suggests a rethinking of the categories, including giving more attention to indigenous religions.