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Reptiles exhibit high species richness and endemism in deserts of northern Mexico. However, high species richness does not necessarily represent the taxonomic diversity of this group in the context of the regional reptile richness. Here, we determined the species richness, similarly, and taxonomic diversity of Chihuahuan Desert reptile assemblages in nine vegetation types (microphyll xeric scrub, xeric shrub rosette, mezquite, submontane scrub, chaparral, pasture, oak forest, juniper forest, and farmland) occurring in the Guadalcazar region of San Luis Potosi. We found 45 species (24 snakes, 20 lizards, and one turtle). The highest numbers of reptiles were found in microphyll xeric scrub and pasture communities. Chaparral, pasture, and oak forest were most similar in structure and species composition. The richest environments in species were not necessarily the most diverse taxonomically. Submontane scrub and chaparral had smaller numbers of species, but high taxonomic diversity (communities containing species less related to each other taxonomically). In addition, 42.2% of the species are under some threat category in the national red list, 91.1% in the IUCN red list, and all species under some category in the Environmental Vulnerability Score rating system, suggesting that more Natural Protected Areas need to be created in the region, along with strategies for protecting and conserving reptile assemblages and other biotic groups.