We re-examined the biogeography of the leaf-toed geckos (Phyllodactylus) endemic to the Galápagos Islands by analyzing for the first time samples of P. gilberti, a species endemic to Wolf island, in a phylogenetic framework. Our aim was to test the three-colonizations scenario previously proposed for these lizards and estimate the age of each colonization event. To achieve this we estimated simultaneously a species tree and divergence times with Bayesian methods. Our results supported the three-colonizations scenario. Similar to a previous hypothesis, the species tree obtained here showed that most species of Phyllodactylus are nested in a single clade with an age between 5.49 and 13.8 Ma, whereas a second independent colonization corresponding to P. darwini from San Cristóbal island occurred 3.03 Ma ago. The species from Wolf island, P. gilberti, stems from a more recent colonization event (0.69 Ma). Thus, present diversity of Galápagos leaf-toed geckos stems from three independent, asynchronous colonization events. As with other Galápagos organisms, the Pacific coast of South America seems to be the source for the founders of P. gilberti.