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On the geologically new Galápagos Islands Darwin looked for evidence attaching wildlife to an older "centre of creation", and found mockingbirds allied to those in Chile but differing from island to island. He heard that slight variations in the shape of tortoise shells showed which island they came from, but failed to collect them, even after eating tortoises taken on board as food.^[50][51] In Australia the marsupial rat-kangaroo and the platypus seemed so unusual that Darwin thought it was almost as though two distinct Creators had been at work.^[52] He found the Aborigines "good-humoured & pleasant", and noted their depletion by European settlement.^[53]

The Beagle investigated how the atolls of the Cocos (Keeling) Islands had formed, and the survey supported Darwin's theorising.^[49] FitzRoy began writing the official Narrative of the Beagle voyages, and after reading Darwin's diary he proposed incorporating it into the account.^[54] Darwin's Journal was eventually rewritten as a separate third volume, on natural history.^[55]

In Cape Town Darwin and FitzRoy met John Herschel, who had recently written to Lyell praising his uniformitarianism as opening bold speculation on "that mystery of mysteries, the replacement of extinct species by others" as "a natural in contradistinction to a miraculous process".^[56] When organising his notes as the ship sailed home, Darwin wrote that if his growing suspicions about the mockingbirds, the tortoises and theFalkland Islands Fox were correct, "such facts undermine the stability of Species", then cautiously added "would" before "undermine".^[57] He later wrote that such facts "seemed to me to throw some light on the origin of species".^[58]