We describe a new species of Phrynosoma from central northeastern Guerrero, México; perform a phylogenetic analysis of mitochondrial and nuclear sequence data to estimate its phylogenetic relationships; and investigate the monophyly of Phrynosoma asio, P. braconnieri, and P. taurus. The new species can be distinguished from all of its congeners by the possession of a unique combination of morphological characteristics. The molecular genetic data include three fragments of the mitochondrial genome and six nuclear genes (2419 and 3909 base pairs in total, respectively) for 31 samples belonging to the 16 previously recognized species of Phrynosoma and the new species. The new species is strongly supported in maximum likelihood analyses of both the concatenated mitochondrial and nuclear data as a monophyletic, distinct evolutionary lineage sister to, and moderately divergent from, P. taurus, and highly divergent from all of the other species of Phrynosoma. A Bayesian species tree analysis also strongly supports the monophyly of the Brevicauda clade, and a sister relationship between P. taurus and the new species.