Darwin does state in his autobiography, on pages 92-93 that he was a theist, but you really need to read it in context. (Granted I read only the pages just before and after the quote, not the whole book, and not even the footnotes on those pages.)
Another source of conviction in the existence of God, connected with the reason and not with the feelings, impresses me as having much more weight. This follows from the extreme difficulty or rather impossibility of conceiving this immense and wonderful universe, including man with his capacity of looking far backwards and far into futurity, as the result of blind chance or necessity. When thus reflecting I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist.
(from Darwin Online)
If we read farther, we see on pages 93-95:
This conclusion was strong in my mind about the time, as far as I can remember, when I wrote the Origin of Species; and it is since that time that it has very gradually with many fluctuations become weaker. But then arises the doubt—can the mind of man, which has, as I fully believe, been developed from a mind as low as that possessed by the lowest animal, be trusted when it draws such grand conclusions? May not these be the result of the connection between cause and effect which strikes us as a necessary one, but probably depends merely on inherited experience? Nor must we overlook the probability of the constant inculcation in a belief in God on the minds of children producing so strong and perhaps an inherited effect on their brains not yet fully developed, that it would be as difficult for them to throw off their belief in God, as for a monkey to throw off its instinctive fear and hatred of a snake.
I cannot pretend to throw the least light on such abstruse problems. The mystery of the beginning of all things is insoluble by us; and I for one must be content to remain an Agnostic. (Granted, this portion was written in a letter to Francis Darwin [who was editing the autobiography], by Emma Darwin and not actually written by Charles Darwin)
A man who has no assured and ever present belief in the existence of a personal God or of a future existence with retribution and reward, can have for his rule of life, as far as I can see, only to follow those impulses and instincts which are the strongest or which seem to him the best ones. A dog acts in this manner, but he does so blindly. A man, on the other hand, looks forwards and backwards, and compares his various feelings, desires and recollections. He then finds, in accordance with the verdict of all the wisest men that the highest satisfaction is derived from following certain impulses, namely the social instincts. If he acts for the good of others, he will receive the approbation of his fellow men and gain the love of those with whom he lives; and this latter gain undoubtedly is the highest pleasure on this earth. By degrees it will become intolerable to him to obey his sensuous passions rather than his higher impulses, which when rendered habitual may be almost called instincts. His reason may occasionally tell him to act in opposition to the opinion of others, whose approbation he will then not receive; but he will still have the solid satisfaction of knowing that he has followed his innermost guide or conscience.—As for myself I believe that I have acted rightly in steadily following and devoting my life to science. I feel no remorse from having committed any great sin, but have often and often regretted that I have not done more direct good to my fellow creatures. My sole and poor excuse is much ill-health and my mental constitution, which makes it extremely difficult for me to turn from one subject or occupation to another. I can imagine with high satisfaction giving up my whole time to philanthropy, but not a portion of it; though this would have been a far better line of conduct.
Nothing is more remarkable than the spread of scepticism or rationalism during the latter half of my life. Before I was engaged to be married, my father advised me to conceal carefully my doubts, for he said that he had known extreme misery thus caused with married persons. Things went on pretty well until the wife or husband became out of health, and then some women suffered miserably by doubting about the salvation of their husbands, thus making them likewise to suffer.
If we read in context we can see not only that Darwin doubts the human capacity to comprehend God, and the freedom of the choice to believe. He reaffirms his belief in the evolutionary ancestry of humans, and depicts himself as:
A man who has no assured and ever present belief in the existence of a personal God or of a future existence with retribution and reward
This is the answer to the question as put, but some more perspective should be given. Even if Darwin believed in God, even the Christian God as depicted by the 19th century Anglican Church, it doesn't mean that his scientific findings lose their validity. Being an active religious person who participates in active religious life doesn't mean that you must not accept the theory of evolution (assuming this is what the debate was about).
The most notable example for this is Kenneth R. Miller, who is a practicing Roman Catholic evolutionary biologist and was a witness at the Kitzmiller v. Dover Area School District trial opposing the teaching of Intelligent Design in public schools in the US.
He is not the only one: There is a full Wikipedia page dedicated to Roman Catholic scientists, and there are many other scientists of other religions.
Even Richard Dawkins himself collaborates with religious figures. In this video he makes an interview with the Bishop of Oxford, saying that they both have the same view of the physical way the world came into existence, even though they don't have the same moral and religious view.
