In this article, I revise the taxonomy of the species and subspecies of the genus Phrynosoma through phylogenetic and species delimitation approaches based on four mtDNA markers (ND1, ND2, ND4, and 12S). The resulting taxonomy recognizes 12 species (P. asio, P. bracconieri, P. cornutum, P. coronatum, P. douglasii, P. hernandesi, P. mcallii, P. modestum, P. orbiculare, P. platyrhinos, P. solare, and P. taurus). Several of these species are divided into subspecies as follows: P. coronatum (P. c. coronatum, P. c. blainvillii, P. c. cerroense, and P. c. frontale), P. cornutum (P. c. cornutum and P. c. bufonium), P. hernandesi (P. h. hernandesi, P. h. ditmarsi, and P. h. ornatum), P. orbiculare (P. o. orbiculare, P. o. bradti, P. o. boucardii, P. o. cortezii, P. o. dugesii, and P. o. durangoensis), P. platyrhinos (P. p. platyrhinos and P. p. goodei), P. taurus (P. t. taurus and P. t. sherbrookei). In this coherent and objective approach, those taxa treated here as subspecies have diverged to a much lesser degree than those that are herein recognized as separate species. Typically, those taxa recognized as subspecies are one another’s closest relatives (i.e., they together form a monophyletic group that represents the species) and are distributed allopatrically. In this approach, all separate evolutionarily significant units are recognized as named taxa—either species or subspecies—thereby reflecting the importance of identifying and naming such units for conservation. I provide a checklist of the recognized species and subspecies of Phrynosoma along with synonymies and distribution maps.