The Voyage of the HMS Beagle 1831-36 Armadillos and fossil Glyptodonts. Both found in the same locations in South American. If these had been created separately, why would both living and extinct forms be restricted to the same area. Darwin thought it made more sense to assume the armadillo evolved from the glyptodon. Each island has a slightly different species of finch, all of which appear close to a single species found on the South American mainland.
Fossils show multiple examples of transitional forms.
Evidence from animal breeding Darwin was greatly impressed by how much domesticated animals had been changed by artificial selection. The biochemistry of a bat is much closer to that of a whale, rather than a bird. Not expected unless bat and whale have a more recent common ancestor than bat and bird, but evolution predicts this.