A selection of letters that give a good introduction to the subject of Darwin and religion:
Letter 441: Emma Wedgwood to Darwin, [21–22 Nov 1838]
Darwin became engaged to his cousin, Emma Wedgwood, on 11 November 1838. Emma wrote to Charles shortly thereafter, concerned that their religious differences would make a painful divide between them.
My reason tells me that honest & conscientious doubts cannot be a sin, but I feel it would be a painful void between us. I thank you from my heart for your openness with me & I should dread the feeling that you were concealing your opinions from the fear of giving me pain.
Letter 471: Emma Darwin to Charles Darwin [c. Feb 1839]
Immediately following her marriage to Charles, Emma writes about the danger of a scientific frame of mind infringing upon the religious domain.
May not the habit in scientific pursuits of believing nothing till it is proved, influence your mind too much in other things which cannot be proved in the same way, & which if true are likely to be above our comprehension.
Letter 2534: Charles Kingsley to Darwin, 18 Nov 1859
In 1859, Darwin sent a copy of Origin of Species to the Anglican clergyman and naturalist Charles Kingsley, who wrote to thank him for the “unexpected honour”, and remarked:
I have gradually learnt to see that it is just as noble a conception of Deity, to believe that he created primal forms capable of self development into all forms needful pro tempore & pro loco, as to believe that He required a fresh act of inter-vention to supply the lacunas wh. he himself had made. I question whether the former be not the loftier thought.
Darwin added this sentence (slightly reworded), as from “a celebrated author and divine”, to the 2d. edition of Origin (p. 481).
Letter 2548: Adam Sedgwick to Darwin, 24 Nov 1859
One of Darwin’s mentors at Cambridge, the professor of geology Adam Sedgwick, also received a presentation copy of Origin, but expressed his great dissatisfaction with the book, especially its neglect of the moral aspect of nature.
Tis the crown & glory of organic science that it does thro’ final cause , link material to moral; & yet does not allow us to mingle them in our first conception of laws … You have ignored this link; &, if I do not mistake your meaning, you have done your best in one or two pregnant cases to break it. Were it possible (which thank God it is not) to break it, humanity in my mind, would suffer a damage that might brutalize it—& sink the human race into a lower grade of degradation than any into which it has fallen since its written records tell us of its history.
Letter 2814: Darwin to Asa Gray, 22 May 
Darwin discussed the religious implications of his theory most openly with the American botanist Asa Gray, a strong supporter of Darwin’s work and an ardent Presbyterian. Darwin’s letters to Gray raised questions about the nature and role of God in nature.
I had no intention to write atheistically. But I own that I cannot see, as plainly as others do, & as I shd wish to do, evidence of design & beneficence on all sides of us. There seems to me too much misery in the world…. On the other hand I cannot anyhow be contented to view this wonderful universe & especially the nature of man, & to conclude that everything is the result of brute force. I am inclined to look at everything as resulting from designed laws, with the details, whether good or bad, left to the working out of what we may call chance. Not that this notion at all satisfies me. I feel most deeply that the whole subject is too profound for the human intellect.
Letter 5303: Mary Boole, to Darwin, 13 Dec 1866
Some of Darwin’s readers wrote directly to him with questions about the implications of evolution for religious belief. The educator and author Mary Boole asked if Darwin’s theory of natural selection was consistent with belief in a personal and infinitely good God.
I felt that you had supplied one of the missing links,—not to say the missing link,—between the facts of Science & the promises of religion. Every year’s experience tends to deepen in me that impression.
Letter 5307: Darwin to Mary Boole, 14 Dec 1866
Darwin was very reluctant to make public statements about the possible bearing of his work on religion, but he almost always replied to correspondents, however briefly. He answered Mary Boole’s letter, adding that his opinion was “not worth more than that of any other man who has thought on such subjects”.
I may however remark that it has always appeared to me more satisfactory to look at the immense amount of pain & suffering in this world, as the inevitable result of the natural sequence of events, i.e. general laws, rather than from the direct intervention of God…. I thank you for your Judgment & honour you for it, that theology & science should each run its own course & that in the present case I am not responsible if their meeting point should still be far off.
Letter 5500: Darwin to Ernst Haeckel, 12 Apr 
Darwin was sometimes criticized for using a humble and conciliatory style of argument, which potentially lent strength to his opponents. But Darwin believed that a more aggressive conduct of debate was often harmful and ineffective. In this letter, he offers criticism and advice to one of his most combative supporters, the German zoologist Ernst Haeckel.
I know that it is easy to preach & if I had the power of writing with severity I dare say I shd triumph in turning poor devils inside out & exposing all their imbecility. Nevertheless I am convinced that this power does no good, only causes pain. I may add that as we daily see men arriving at opposite conclusions from the same premises it seems to me doubtful policy to speak too positively on any complex subject however much a man may feel convinced of the truth of his own conclusions.
Letter 12041: Darwin to John Fordyce, 7 May 1879
Darwin regarded religious belief as a personal and private matter. In this letter to the writer John Fordyce, he gives a rare account of his religious views, settling on a term that had been recently coined by Thomas Henry Huxley: “agnostic”.
What my own views may be is a question of no consequence to any one except myself.— But as you ask, I may state that my judgment often fluctuates…. In my most extreme fluctuations I have never been an atheist in the sense of denying the existence of a God.— I think that generally (& more and more so as I grow older) but not always, that an agnostic would be the most correct description of my state of mind.
Letter 13230: Darwin to William Graham, 3 July 1881
Darwin writes to William Graham, the author The Creed of Science, disputing Graham’s claim that universal laws of nature imply an ultimate purpose for life, and questioning whether inner convictions ought to be trusted, given the animal ancestry of the human mind.
You have expressed my inward conviction, though far more vividly and clearly than I could have done, that the Universe is not the result of chance. But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?