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A new species, Microcavia criolloensis (Rodentia, Caviidae), from the Upper Pleistocene (Sopas Formation) of the northern basin of Uruguay (South America) is described. This species is characterised by an exclusive association of skull and dental state characters. An analysis of similarity including other species of the genus and the related genera of Caviidae was performed. The new species of Microcavia behaved in the phenogram obtained as a discrete unit closely associated to Microcavia chapalmalensis and Microcavia niata. A mosaic of habitats, ranging from open and arid or semiarid microhabitats to fluvial and riparian forests, is suggested here, mainly based on the current adaptations of the genus Microcavia and the records of several taxa of mammals in the Sopas Formation. The geographic area occupied by Microcavia in the Pleistocene was different, with fossil records located more than 500 km eastward with respect to its present distribution. This variation could have occurred as a response to environmental changes in the last interglacial and glacial cycles.