Proctoporus bolivianus is a gymnophthalmid lizard species that occurs at high elevations in the Andes Mountains of southern Peru and Bolivia. Extensive morphological variation in populations collected in the Department of Cusco, Peru, suggested the presence of cryptic species. To assess this possibility, we reconstructed morphological and molecular phylogenies of 13 populations of this species and also used a character-based approach to examine the morphology in more detail. We found P. bolivianus to be composed of three distinct lineages that are separated by substantial genetic distances. We erect two new species to contain unnamed lineages within the P. bolivianus complex. These three species are found within a small geographic area and are likely differentiated because of historical geographic barriers in the extreme landscape of the central Andes.