One of the most useful strategies for biological conservation is the creation of protected natural areas. In addition, periodic updates of management plans are necessary to modify or improve the information and make it accessible to future research. Banco Chinchorro Biosphere Reserve is a protected atoll situated 31 km eastward from the southern coast of Quintana Roo, Mexico. A management plan published in 2000 contains a list of reptiles inhabiting the four islands of the atoll, but concerns about errors contained on the list necessitated updates and corrections. Herein, we clarify and update this list and present new life-history data for some species. We used four approaches to improve the list: interviews with staff, fishermen, and professional visitors; literature review; scientific collections; and field work conducted from 2011 to 2013. Thirteen species (1 crocodilian, 4 marine turtles, 2 iguanas, 2 geckos, 2 anoles, 1 whiptail lizard, and 1 snake) were observed in comparison to 14 species previously recorded in the management plan. Of the 13 species currently noted, 9 (69%) species appear in the International Union for Conservation of Nature Red List (7 with a threatened status), 7 (54%) are in Convention on International Trade in Endangered Species of Wild Fauna and Flora Appendices, and 9 (69%) are protected by Mexican law. One invasive species (Anolis sagrei) seems to have adapted and found its niche; whereas another (Hemidactylus frenatus) represents a threat for another species (Aristelliger georgensis), and efforts to eradicate it are strongly recommended. Banco Chinchorro is the only site in Mexico where Anolis allisoni is present. It also hosts the most distant and isolated population of the parthenogenetic lizard Aspidoscelis maslini from the mainland. After this study, we promoted the inclusion of both species in the Mexican protected species list based on ecological and distribution information. Finally, we discuss considering the reptiles of the reserve as Evolutionarily Significant Units.