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We analyzed the geographic variation in cranial morphology of the Southern Mountain Cavy, Microcavia australis, throughout of its distributional range. Our analysis allows us to recognize three geographically allopatric morphotypes. These morphotypes differ in the general size and shape of the skull and discrete morphological traits of the zygomatic arch, palate and mesopterygoid fossa. Based on these results, we restrict the name australis to populations distributed in southern Argentina and west-central Andes and the name maenas to the morphotype of northwestern and central Argentina. The third morphotype occurs in the Dry Chaco ecoregion and is described here as a new species.