The herpetofauna of the insular systems of Mexico is composed of 226 species, of which 14 are anurans, two are salamanders, and 210 are reptiles, comprised of two crocodilians, 195 squamates, and 13 turtles. Although the surface of the Mexican islands is only 0.26% of the Mexican territorial extension, these 226 species constitute 16.1% of Mexico’s documented herpetofauna of 1405 species. We classified the Mexican islands into five physiographic regions: the islands of Pacific Baja California; the islands of the Gulf of California; the islands of the Tropical Pacific; the islands of the Gulf of Mexico; and the islands of the Mexican Caribbean. The highest species richness among these regions is in the Gulf of California, with 108 species, and the lowest richness is 40 for the islands of the Pacific Baja California and 46 for those of the Gulf of Mexico. We identified introduced species, risk of wildfires, climate change, and urban/tourist development as the main environmental threats impinging on these species. In addition, we assessed the conservation status of the native species by comparing the SEMARNAT (NOM-059), IUCN Red List, and the Environmental Vulnerability Score (EVS) systems. The comparison of these systems showed that the NOM-059 and the IUCN systems seriously underestimate the degree of threat for insular endemics, being particularly concerning for those insular species that are known only from their respective type localities. The EVS system proved to be practical and indicated that 94 species have a high vulnerability status, 62 a medium status, and 56 a low status. The Relative Herpetofaunal Priority system, which contrasts the number of endemic and threatened species among different physiographic areas, indicates that the regions with the highest priority are the Islands of the Gulf of California, followed by the islands of the Tropical Pacific. Finally, we discussed the completeness of the Mexican Natural Protected Areas on the insular systems of the country; the result is outstanding since Mexico is already close to achieving the goal of having all their islands under some degree of federal protection.