Six geographic samples of the fossorial genus Aconaemys were studied to determine differences in cranial morphometrics, pelage coloration, and karyotype. Results showed variation that departs significantly from previous works. Distinct karyotypes were found for each nominal form. Using cluster analysis and discriminant-function analysis, contrasting patterns of cranial morphology are demonstrated that show A. fuscus to be as distinct from A. sagei as is A. porteri. Despite a certain degree of overlap in qualitative cranial characters and pelage coloration, three monotypic species of Aconaemys are recognized.