Problem one: why, if God designed the human mind, did it take so long for humans to develop theistic concepts and beliefs? Problem two: why would God use evolution to design the living world when the discovery of evolution would predictably contribute to so much nonbelief in God? Darwin was aware of such questions but failed to see their evidential significance for theism. This paper explores this significance. Problem one introduces something I call natural nonbelief, which is significant because it parallels and corroborates well-known worries about natural evil. Problems one and two, especially when combined, support naturalism over theism, intensify the problem of divine hiddenness, challenge Alvin Plantinga’s views about the naturalness of theism, and advance the discussion about whether the conflict between science and religion is genuine or superficial.