Around 19–22% of reptiles worldwide are in danger of disappearing. This problem also occurs in Mexico, particularly in Chiapas, which boasts the second-highest number of recorded reptile species in the country. To address this issue, we conducted a study to determine how natural areas can help to protect these reptiles in the state. We compiled a database of 217 reptile species in Chiapas to create Species Distribution Models (SDMs). We analyzed representativeness, beta diversity, and species richness. Our findings showed a high level of representativeness for the records and species distribution models. By stacking the maps with the total number of endemic and threatened species, we identified two hot spots for the study area, i.e., the Northern Highlands, the Central Depression, and the Sierra Madre de Chiapas. Based on the SDMs, we found more endemic and threatened species within protected natural areas than outside of these. Our study can help prioritize conservation efforts in little-studied protected areas and reaffirm the importance of conservation in areas such as the Biosphere Reserve Selva El Ocote, home to a diverse range of endemic and threatened species.