Chelemys macronyx is a medium-sized, long-clawed sigmodontine of fossorial habits, distributed between 33 degrees 20' and 51 degrees 30'S in the central and southern Andes of Argentina and Chile. Phylogeographic studies based on the analysis of mitochondrial DNA showed that this rodent has a shallow genealogy geographically structured into two main clades: one in the northern part of its range, at high-Andean localities in the Argentinean provinces of Mendoza and northern Neuquen, and the other covering medium- to low-elevation areas from northwestern Neuquen to southern Chile and Argentina. Qualitative and quantitative morphological characters show the existence of two main morphotypes of C. macronyx. Northern populations are characterized by a mesopterygoid fossa rounded at its anterior border and by a large and nearly circular foramen ovale, whereas in central and southern populations the mesopterygoid fossa is quadrate with an ovate to piriform foramen ovale. The described morphological variation is in congruence with the phylogeographic patterns identified by molecular markers. In light of these results, we suggest a simplified taxonomic arrangement on which two subspecies are recognized within C. macronyx, a northern one and a southern one for which the names C. m. macronyx and C. m. vestitus correspond, respectively.