<p>Land use change drives biodiversity loss, but fragmented landscapes can still support substantial biodiversity. To explore the dynamics between landscape characteristics and diversity, multi-scale analyses are needed. We examined reptile taxonomic and functional diversity in two subtropical landscapes within the Sierra Madre del Sur, a biodiverse region in southern Mexico with urgent conservation needs. Reptile communities were surveyed across various land use types, and predictor variables were analyzed at local and landscape scales. Functional trait variations between land use types were examined, and functionally unique, specialized, and endangered species were identified. Higher taxonomic/functional diversity was observed in forest patches compared to croplands and non-natural pastures, though common species/functional groups were more diverse in the latter. We observed greater trait diversity in forest patches, as well as functionally specialized, unique, and endangered species. Reptile abundance and diversity were positively related to local vegetation and forest cover within 100–500&#xa0;m landscape scales. At larger spatial scales, the presence of other land use types was an important driver of overall diversity. These findings underscore the conservation value of both large and small forest patches for reptile conservation, which may be serving as source habitats for disturbed land uses. However, at broader scales, a more heterogeneous landscape may enhance overall diversity, so efforts should consider the conservation value of other land use types within the landscapes. A holistic conservation approach, integrating landscape-scale factors and local variables, is essential for understanding and preserving reptile diversity in these fragmented landscapes.</p>