The genus Proctoporus sensu stricto is a poorly known gymnophthalmid lizard clade distributed across the Andes of southern Peru and Bolivia. Recent collecting efforts in central and southern Peru recovered specimens and tissues of all known members of the genus, enabling the first complete phylogeny of the genus to be constructed. In addition, a new species was found in Puno, Peru and is described herein. We analyzed DNA sequences of three mitochondrial genes using maximum parsimony and Bayesian MCMC methods to reconstruct a phylogeny of the group. The phylogeny suggests an ancient split between a newly discovered lineage from Puno and the remaining species that coincides geographically with its isolated range. Proctoporus pachyurus and P. sucullucu form sister species; P. bolivianus forms a clade with P. unsaacae P. guentheri. The elevationally restricted ranges of all known Proctoporus species likely have contributed to the high species diversity found in southern Peru. Both allopatric and parapatric modes of speciation are proposed to explain the diversification of Proctoporus species.