Terrestrial squamate reptiles from the Galápagos archipelago have limited gene flow among islands, providing an opportunity to test paleogeographic models. Previous work suggests that Pleistocene glaciations had a strong influence on the evolution of Galápagos’ land-locked vertebrates, such as lizards and snakes, by allowing dispersal and contact among populations from different islands or islets through land connections. One prediction of this model is that extant populations, despite being isolated at present, are genetically similar due to recent (Pleistocene) gene flow. Here we test this prediction with a simple comparative phylogeographic analysis of two sympatric lizards from Floreana island and surrounding islets. Based on two mitochondrial genes, we show that Floreana lava lizards (Microlophus grayii) and leaf-toed geckos (Phyllodactylus baurii) from Floreana Island are very similar genetically to conspecifics from Champion, an islet in the Floreana group that was connected to Floreana during Pleistocene glacial maxima. Moreover, they are significantly less similar to conspecifics from Gardner, an islet in the Floreana group that was not in contact with Floreana during Pleistocene glacial maxima. Thus, our results support the idea of Pleistocene glaciation-driven contact among populations from different islands in the Floreana cluster with no identifiable subsequent dispersal. These results also show that Floreana and Champion populations are part of the same evolutionary significant unit for both species, which might be at risk due to an upcoming invasive mammal eradication program in Floreana. Therefore, Champion represents a reasonable source for potential reintroductions of both lava lizards and leaf-toed geckos into Floreana.