Darwin didn't walk around the Galapagos and come up with the theory of evolution. He was exploring, collecting, making observations. It wasn't until he got back and went through the samples that he noticed the differences among them and put them in context.

The starting point of Darwin's theory of evolution is precisely the existence of those differences between individual members of a race or species which morphologists for the most part rightly neglect. The first condition necessary, in order that any process of Natural Selection may begin among a race, or species, is the existence of differences among its members; and the first step in an enquiry into the possible effect of a selective process upon any character of a race must be an estimate of the frequency with which individuals, exhibiting any given degree of abnormality with respect to that, character, occur. The unit, with which such an enquiry must deal, is not an individual but a race, or a statistically representative sample of a race; and the result must take the form of a numerical statement, showing the relative frequency with which the various kinds of individuals composing the race occur.