This study seeks to clarify the taxonomic identity of three adult frogs and two tadpoles from Rara Lake situated in Rara National Park, Mugu district, Western Nepal, using both phenotypic and mitochondrial sequence data (16S rRNA gene). Based on the molecular data, we determined our specimens belonged to two species; Paa cf. ercepeae (Dubois, 1974) and Paa rarica (Dubois, Matsui, and Ohler, 2001), and this assignment is also supported by morphology. Principal component analysis of phenotypic data clustered species into large-bodied (SVL > 55 mm) and small-bodied (SVL < 55 mm) groups. The molecular data suggest that Paa rarica belonged to a group that contains several undescribed lineages and that Paa liebigii (Gnther, 1860) hosts extensive cryptic diversity. Our study also documents that Paa species in the Himalayan region are more widely distributed than previously believed.