In this paper, I will explore the relationship between Darwin’s evolutionary theory and his religion. Was Darwin an atheist as Dawkins claimed in his Blind Watchmaker? Was Paley’s natural theology simply discarded by Darwin and replaced with natural selection as Dawkins claimed in his God Delusion? How did Darwin himself view religion and evolution? These questions have been the focus of intense studies since Canon’s pioneering work appeared in 1960s. Based on theses works and also Darwin’s correspondence and note books, this paper will show that Darwin was not an atheist and that natural theology played an important part in the development of Darwin’s theory of natural selection in both positive and negative ways.