South American leptodactylid frogs of the genus Phrynopus occur in cloud-forest, páramo, subpáramo and puna habitats (1000–4400 m elevation) from Colombia to Bolivia. Currently, there are 34 described species; however, many additional species new to science have been reported from Colombia, Peru, and Bolivia. The phylogeny of the species-diverse Phrynopus is unknown and the position of the genus within Leptodactylidae is poorly understood. We present the results of a phylogenetic study based on 12S and 16S mitochondrial rDNA. Fifteen species of Phrynopus from Bolivia to Ecuador are included, along with several other genera of Leptodactylidae and representatives of other frog families. Our results indicate that Phrynopus is phylogenetically nested within Eleutherodactylus, whereas Phyllonastes is phylogenetically nested within Phrynopus. Based on the recovered phylogeny, we transfer Phrynopus simonsii to Eleutherodactylus, and show that Phrynopus carpish needs to be removed from Phrynopus. Eleven of the 13 Phrynopus species occurring in Central Peru share the absence of an external and internal ear.