This paper discusses the relationship between religion and science education in the light of the cognitive sciences. We challenge the popular view that science and religion are compatible, a view that suggests that learning and understanding evolutionary theory has no effect on students' religious beliefs and vice versa. We develop a cognitive perspective on how students manage to reconcile evolutionary theory with their religious beliefs. We underwrite the claim developed by cognitive scientists and anthropologists that religion is natural because it taps into people's intuitive understanding of the natural world which is constrained by essentialist, teleological and intentional biases. After contrasting the naturalness of religion with the unnaturalness of science, we discuss the difficulties cognitive and developmental scientists have identified in learning and accepting evolutionary theory. We indicate how religious beliefs impede students' understanding and acceptance of evolutionary theory. We explore a number of options available to students for reconciling an informed understanding of evolutionary theory with their religious beliefs. To conclude, we discuss the implications of our account for science and biology teachers.