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The closest living relative (though not a direct ancestor) of the Galápagos giant tortoise is the Chaco tortoise (Chelonoidis chilensis), a much smaller species from South America. Mitochondrial DNA analysis indicates that the oldest existing islands (Española and San Cristóbal) were colonised first, and that these populations seeded the younger islands via dispersal in a "stepping stone" fashion via local currents.Restricted gene flow between isolated islands then resulted in the independent evolution of the populations into the divergent forms observed in the modern species.Garman proposed the linking of nigra with the extinct Floreana species.Later, Pritchard deemed it convenient to accept this designation, despite its tenuousness, for minimal disruption to the already confused nomenclature of the species.

Survival on the 1000-km oceanic journey is accounted for because the tortoises are buoyant, can breathe by extending their necks above the water, and are able to survive months without food or fresh water. nigra probably occurred 6–12 million years ago, an evolutionary event preceding the volcanic formation of the oldest modern Galápagos Islands 5 million years ago.The evolutionary relationships between the species thus echo the volcanic history of the islands.The five populations living on the largest island, Isabela, are the ones that are the subject of the most debate as to whether they are true species or just distinct populations or subspecies.The extinction of most giant tortoise lineages is thought to have also been caused by predation by humans or human ancestors, as the tortoises themselves have no natural predators.Tortoise populations on at least three islands have become extinct in historical times due to human activities.

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