Darwin never claimed to be an atheist. Very late in life, he said he was leaning toward agnosticism.
From the autobiography:
"1828-1831.—After having spent two sessions in Edinburgh, my father perceived, or he heard from my sisters, that I did not like the thought of being a physician, so he proposed that I should become a clergyman. He was very properly vehement against my turning into an idle sporting man, which then seemed my probable destination. I asked for some time to consider, as from what little I had heard or thought on the subject I had scruples about declaring my belief in all the dogmas of the Church of England; though otherwise I liked the thought of being a country clergyman. Accordingly I read with care Pearson on the Creed, and a few other books on divinity; and as I did not then in the least doubt the strict and literal truth of every word in the Bible, I soon persuaded myself that our Creed must be fully accepted."
You can find his autobiography here:
http://www.stephenjaygould.org/library/ ... raphy.html
It's not very long, and it has no statement of atheism.
Darwin, in "The Origin of Species", gave credit to God for creation, so we can be sure he was a believer when he came up with his theory.