The giant tortoises of the Galápagos Archipelago influenced Darwin's early thinking on transmutation and now constitute a famous example of island-based speciation and evolutionary dynamics. Questions regarding their evolutionary origin still exist and include whether their giant size evolved before or after the lineage arrived in the Galápagos from the South American continent. Here we present new evidence supporting the ‘before’ hypothesis based on previously reported fossil specimens from the Late Pleistocene of Ecuador. Despite the isolated and fragmentary nature of these tortoise fossils, phylogenetically informative features are preserved. A tip-dated phylogenetic analysis recovers the Ecuador form as the sister taxon to the Galápagos lineage, thus supporting the existence of a closely related, giant tortoise population at approximately the same time and place that the Humboldt Current is thought to have carried the ancestral Galápagos tortoise to the archipelago. The phylogeny also raises the possibility that the same evolution of continental gigantism also facilitated the dispersal of South American tortoises into the Caribbean Basin where they diversified before succumbing to Holocene extinction.