The southern pygmy mouse, Baiomys musculus, is distributed in arid and semiarid lowlands, from southern Nayarit and central Veracruz in México to northwestern Nicaragua, excluding the Yucatán Peninsula and the Caribbean tropical lowlands. Previous reports suggest that B. musculus includes two clades that may be eligible for specific status, although this remains uncertain. We used mitochondrial DNA (cytochrome b) and morphometric data to test whether two lineages exist within the species. Molecular data support the existence of two monophyletic groups with genetic distances of 6.69 % between them: clade I, a western clade found in Colima, Jalisco, and Michoacán; and clade II, an eastern clade found in Guerrero, Morelos, Oaxaca, and Veracruz. Morphologically, clade I individuals are larger than clade II. Moreover, these clades seem to be allopatric, and their geographic boundaries are located in the complex topography of western México. Examination of previous reviews in addition to the data from this study suggest that it may be appropriate to recognize each clade as a species: clade I as B. musculus (Merriam, 1892) and clade II as B. brunneus (Allen and Chapman, 1897). Future studies with nuclear or genomic data, including Central American populations, would verify this taxonomic hypothesis.