The Origin of the Species was published in 1859, 24 years after Darwin's 5 week long visit to the Galapagos. During the intervening years Darwin had deepened his argument for natural selection to the extent that the Galapagos actually became a small part of the book: mentioned in all 6 times, all towards the end.
Laura, Thank you for your interest concerning our Galapagos cruise. The time there was really interesting and we enjoyed our stay. Best regards, Ralf and Marga