Cranial and external morphology of 54 specimens of rodents of the genus Akodon from southern Brazil was analyzed. The sample included 27 individuals with a karyotype of 2n = 44 and 13 with 2n = 46 and 14 nonkaryotyped animals. Principal components analysis separated individuals with 2n = 44 from those with 2n = 46. Individuals with 2n = 44 were distinguished from those with 2n = 46 by narrow and elongated molars, ectolophid present, narrow interorbital breadth, reduced tegmen tympani, and distal baculum with the central and lateral digit approximately equal in size and proportions, not enlarged in the extremity. Discriminant functions analyses including 6 A. sanctipaulensis individuals and holotypes of A. serrensis and A. s. leucogula resulted in 3 distinct groups. The 2n = 46 individuals were related to A. serrensis, but those with 2n = 44 were not assignable to any described species for Akodon. We describe and propose the recognition of a new species for the genus.