Reptiles are one of the most diverse groups of vertebrates in the world that are distributed in almost all ecosystems. Many of these studies have focused on exploring their diversity patterns across different environments; and recent studies on reptile alpha and beta diversity have incorporated a multifaceted approach into their analysis to have more comprehensive evaluations. This study presents an assessment of the taxonomic diversity of reptile patterns using methods that incorporate the assessment of higher taxa. Likewise, the taxonomic dissimilarities between reptile communities in the physiographic regions of the state of Jalisco were analyzed. Evaluations for the groups of snakes and lizards independently are presented. We use the taxonomic distinctiveness index that assesses the complexity of the taxonomic structure of communities through hierarchical classification above the species level to measure the relationships between taxa. The dissimilarity of the taxonomic structure in each community was also analyzed. Beta diversity partitions were performed to identify the contribution of turnover and the differences in richness. We determined that alpha diversity of species and higher taxa maintain different patterns, indicating that Jalisco presents regions with overrepresentation of reptile families and genera, as well as regions with an opposite trend. The representation of higher taxa is higher in the lizard group, although in terms of species richness snakes are the most prominent group. The turnover is the most important component at species and higher taxa, with similar values for lizards and snakes. The findings presented show that incorporating phylogenetic information about species through taxonomic relationships provides complementary information that species diversity per se, especially at the level of alpha diversity.