Although Darwin believed the theory he proposed in his book
The Origin Of Species
This book is promoted as the bible for evolution but it actually has evidence against evolution. I'll quote a few excerpts from chapters six and nine where he talks about the problems with the theory of evolution.
Here is what I consider the most important excerpt of the book:
"Why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms."
This is from chapter 6 entitled Difficulties on the Theory. He expects to see certain evidence in the fossil record if his theory is true, but it is not there. There are two chapters devoted to the problems with the theory. Here are more excerpts from those chapters:
"To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree."
"If numerous species, belonging to the same genera or families, have really started into life all at once, the fact would be fatal to the theory to descent with slow modification though natural selection."
"I concluded that this great group had been suddenly developed at the commencement of the tertiary series This was a sore trouble to me, adding as I thought one more instance of the abrupt appearance of a great group of species. "
"The case most frequently insisted on by paleontologists of the apparently sudden appearance of a whole group of species, is that of the teleostean fishes, low down in the Chalk period."
"On the sudden appearance of groups of Allied Species in the lowest known fossilferous strata: There is another and allied difficulty, which is much graver. I allude to the manner in which numbers of species of the same group suddenly appear in the lowest known fossiliferous rocks."
"Consequently, if my theory be true, it is indisputable that before the lowest Silurian stratum was deposited, long periods elapsed, as long as, or probably far longer than, the whole interval from the Silurian age to the present day; and that during these vast, yet quite unknown, periods of time, the world swarmed with living creatures. To the question why we do not find records of these vast primordial periods, I can give no satisfactory answer."
"The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained."
"The several difficulties here discussed, namely our not finding in the successive formations infinitely numerous transitional links between the many species which now exist or have existed; the sudden manner in which whole groups of species appear in our European formations; the almost entire absence, as at present known, of fossiliferous formations beneath the Silurian strata, are all undoubtedly of the gravest nature."
Darwin was concerned that the lack of transitional fossils disproved the theory. He hoped that in the years to come there would be more fossil finds that would prove the theory as he stated it. It has been about 150 years since he wrote that book, and countless more fossils have been found as people search for missing links, but the innumerable transitional forms have not been found. Darwin says himself the lack of these fossils would be fatal to the theory.
I discuss the fossil record more on this page: What Is the Cambrian Explosion?