The Colombian leaf-toed gecko (Phyllodactylus transversalis) is the least known reptile species of Malpelo Island (Eastern Tropical Pacific). In the 37 years since its original description, no single study strictly dedicated to this species has been conducted. With the goal of providing information on the ecology and population size of this gecko, data collected during two visits to the island are presented. Behavior and reproduction were studied by following individuals during the night and by searching for hidden individuals and eggs during the day. Population’s density and habitat preferences were estimated by classifying the island’s surfaces into four types and counting geckos inside those habitats within band transects. General morphological measurements of geckos were performed as reference points for future comparisons. Phyllodactylus transversalis lays its eggs in narrow crevices of rocks, apparently communally. Reproduction seems to take place during most of the year, probably associated with the peak breeding season of seabirds. Although conspecifics shared shelters during the day, densities during the night suggest no apparent habitat preference for foraging. Population size of this species was estimated at approximately 114000 individuals.