<p>The geological origin of Mexico involves the formation of large and complex mountain systems located practically throughout its territory. Some of the major systems are the Sierra Madre Occidental (SMOC), Oriental (SMOR), Southern (SMS), and Trans-Mexican Volcanic Belt (FVT). Across these biogeographic areas, we explored patterns of species richness and distinctiveness, and average taxonomic variation of amphibian and reptile communities. Finally we use the Gi* algorithm to suggest areas of high species richness or hotspots intended for the conservation through these mountain systems. We found that the SMOR and FVT have the highest species richness of both groups and a greater similarity in beta diversity explained by the turnover component. After analyzing taxonomic distinctiveness, new areas of importance for conservation in the SMOC were identified, with mountainous areas with a slope toward the Pacific being considered sites of high interest for conservation. These results may represent vicariance events on each mountain system, which have contributed to the differentiation of the herpetofauna of western and northeastern Mexico. The results of this study show the importance of exploring the taxonomic richness of amphibians and reptiles across different mountainous regions of Mexico, allowing for the location of high priority conservation sites for the biodiversity of central and northern Mexico.</p>