Cryptic diversity is frequent among lizards from the Neotropical region. In particular, geckos belonging to the genus Homonota exhibit high levels of phenotypic and ecological conservatism. Homonota uruguayensis is endemic to rocky outcrops in the Uruguayan Savanna, and a previous study based on mitochondrial DNA (mtDNA) revealed a highly divergent clade in an isolated population. In this study, we used a set of two mitochondrial (Cytb and 12S) and six autosomal (DMLX, MXRA, PRLR, SNCAIP, H19B and H30B) genetic markers to evaluate the taxonomic status of different populations of H. uruguayensis. We then used morphological data to further check the favoured coalescent model of species delimitation. A careful re‐evaluation of meristic and continuous morphological traits within the H. uruguayensis complex indicated that the new species can be morphologically distinguished. The species tree confirmed the deep divergence times associated with the new species previously reported for mtDNA and indicated congruence among independent gene trees. Overall, the results clearly support the recognition of a new species, based on deep genetic divergence and morphological differentiation. While the full geographic range of the new species has not been thoroughly characterized, the localized endemism in a patch of rocky outcrops surrounded by intense silviculture activity strongly suggest that the new species should be considered to be under some degree of threat.