The theory of evolution is one of the great intellectual revolutions of human history, drastically changing our perception of the world and of our place in it. Charles Darwin put forth a coherent theory of evolution and amassed a great body of evidence in support of this theory. In Darwin's time, most scientists fully believed that each organism and each adaptation was the work of the creator. Linneaus established the system of biological classification that we use today, and did so in the spirit of cataloguing God's creations.
In other words, all of the similarities and dissimilarities among groups of organisms that are the result of the branching process creating the great tree of life were viewed by early 19th century philosophers and scientists as a consequence of omnipotent design.