We describe a new species of leaf-toed gecko of the genus Phyllodactylus from María Cleofas Island, the smallest island of Tres Marías Archipelago, Nayarit, México. Genomic, phylogenomic, and morphological evidence support that the new species presents a unique combination of diagnostic characters. Morphologically, the new species has a high number of tubercles, head to tail (mean 47), longitudinal ventral scales (mean 61), and third labial–snout scales (mean 26). Gene flow tests revealed the genetic isolation of insular populations from mainland counterparts. In addition, we confirmed the non-monophyly of P. homolepidurus and P. nolascoensis, and we show that the taxon P. t. saxatilis is a complex; therefore, we propose taxonomic changes within the saxatilis clade. The discovery of this new insular endemic species highlights the urgency of continued exploration of the biological diversity of island faunas of Mexico.

We provide an updated checklist of amphibians and reptiles from Isla María Cleofas, Mexico. This island is located at the Islas Marías Archipelago Biosphere Reserve on the coast of the state of Nayarit. The herpetofaunal diversity of Isla María Cleofas has been addressed for over a century; however, the literature is limited just a few scientific explorations and occasional records. In addition, previous herpetofaunal lists contain taxonomic inaccuracies, which are revised here, and recent nomenclatural changes are incorporated. Records of three newly reported species, Lampropeltis polyzona Cope, 1860, Leptophis diplotropis (Günther, 1872) and Tantilla calamarina Cope, 1866, were obtained during our fieldwork. Based on both our field observations and a literature review, the herpetofauna of Isla María Cleofas includes 16 species (two amphibians and 14 reptiles). We also review the conservation status of all species using three independent systems [NOM 059-SEMARNAT-2010, IUCN, and environmental vulnerability score (EVS)]. Finally, we discuss the likely occurrence of evolutionary independent lineages on the island.