Sympatric species of vesper mice (Calomys expulsus and C. tener) from the Cerrado biome are often distinguished by their respective sizes. Using geometric morphometrics, we tested if interspecific differences were mainly due to isometric or allometric size variations or allometry-free shape differences. To delimit species groups, we used and compared linear discriminant analysis, calculated on subsets of individuals of known identity, and pattern recognition techniques, needing no prior information on specimens. They both yielded similar results, indicating that patterns of interspecific morphological differences are mainly due to size-free shape differences located at landmarks defined at the suture between the frontals and the parietals and between the latter and the interparietal. Correct specimen identification was obtained with pattern recognition techniques using Gaussian mixture models. Morphological differences also were found between the 2 species analyzed and the newly described C. tocantinsi represented here by its paratypes. The combination of geometric morphometrics and pattern recognition techniques seems suitable for systematic analyses aimed at elucidating interspecific patterns of morphological variation in closely related species in field studies and museum specimens.