A recent systematic revision pointed out that the name Boana polytaenia has been applied to a nonmonophyletic assemblage because populations identified as B. polytaenia from the northern Mantiqueira and southern Espinhaço mountain ranges are not closely related with the species' nominal clade. In this sense, specimens from these two biogeographic regions were recovered within two clades named Boana sp. 3 and Boana sp. 4, respectively. Here we characterized and compared external morphologies, calls, and DNA of specimens of the clade of B. polytaenia and from the two candidate species (Boana sp. 3 and Boana sp. 4). From these comparisons we herein describe a new cryptic species. Boana guarinimirim sp. nov. differs from its closely related species by the presence of a supracloacal crest, calcar appendage, and conspicuous discs on toes. Nevertheless, the new species could not be completely discriminated from its distantly related taxon B. polytaenia. We applied the new name to the clade distributed throughout the northern Mantiqueira range (Boana sp. 3), but the new name could also be applied to the clade from southern Espinhaço range (Boana sp. 4). Additional sampling efforts and new sources of evidence, such as larvae morphology and chromosomal features, should evaluate whether the lineages are conspecifics.