Reptiles are threatened by anthropogenic landscape transformation, largely due to agriculture. However, ecosystems nowadays constitute a matrix of fragmented landscapes. We analyzed a heterogeneous landscape’s reptile taxonomic and functional diversity patterns across ten land cover/use types in Jalisco state, in west-central Mexico. At the alpha diversity level, we assessed the taxonomic diversity using q-order indices, and functional diversity with multidimensional indices (FRic, FDiv, and FEve) by land cover/use. We evaluated the differences in species composition among land cover/use types (beta diversity). We utilized multidimensional distance-based analyses (dbRDA) to evaluate the association between reptile diversity, habitat structure, and environmental variables. Species richness did not correlate with functional richness across land cover types overall, except for riparian habitat surrounded by crops (RH-C), which exhibited higher species richness and functional diversity. Secondary vegetation surrounded by temperate forest (SV-TF), riparian habitat surrounded by tropical dry forest (RH-TDF), and RH-C were the land cover/use types with the most functional groups. Herbaceous cover is crucial for preserving both reptile diversity facets in this landscape. These findings suggest that the availability of resources (e.g., riparian habitat and herbaceous cover) regardless of perturbation level could be more relevant for reptile diversity than the condition (tropical vs. temperate) due to the high plasticity and adaptation of the group. It is essential to recognize the ecological value of these habitats by adopting a holistic approach that values the intrinsic and ecological importance of reptile diversity.