Glans penis morphology has been used as a powerful tool in mammal taxonomy to differentiate cryptic species. Neotropical rodent species Akodon cursor and A. montensis are cryptic, and interspecific hybrids are like their parental species. We investigated non-metric and metric phallic characters aiming to differentiate A. cursor from A. montensis. We also evaluated the parental species’ influence of the phallic characters on hybrids. We analysed 96 male adults—56 A. cursor, 27 A. montensis, and 13 hybrids, subgrouping species by locality and hybrids by parental species (paternal vs maternal). We verified that A. cursor and A. montensis are distinguishable by penile-shape morphology: A. cursor has an elongated penile form with a flare in the distal portion and A. montensis has a barrel-shaped form. Also, dark spots in ventral view, if present in A. montensis, distinguish A. montensis from A. cursor. Although the non-metric characters differentiate the species, they do not distinguish the subgroups of A. cursor, A. montensis, and hybrids. The metric phallic characters indicated a significant difference between species and hybrids. These characters also differentiate the population groups of A. cursor. However, A. montensis subgroups and hybrids subgroups did not present a significant difference. This study shows the importance of penis morphology in the taxonomy of the cryptic rodent species A. cursor and A. montensis, representing a powerful tool to discriminate male specimens in mammal collections without karyotyping or sequencing, even though the specimens occurred in sympatric areas. Since most taxidermy protocols do not preserve the penis in mammal preparations, liquid preservation of some specimens or the removal of the penis before taxidermy for liquid preservation could be beneficial. We also recommend the organisation in museum collections of a penis bank for the A. cursor species group (or even all rodent species) to avoid losing this important information for species identification.
