To assess genic differentiation and phylogenetic relationships among selected species in the subgenus Aporodon, we screened 31 presumptive genetic loci in 6 species in the subgenus Aporodon (R. creper, R. gracilis, R. mexicanus, R. microdon, R. spectabilis, and R. tenuirostris) and in 4 species in the subgenus Reithrodontomys (R. chrysopsis, R. fulvescens, R. megalotis, and R. sumichrasti). The resulting phylogenetic trees were compared with the results of previous molecular and morphological studies. Results demonstrate that the subgenus Aporodon is monophyletic. Relationships determined on the basis of allozymes are largely congruent with an earlier analysis based on morphological and molecular characters. However, samples of R. mexicanus do not form a monophyletic lineage. Accordingly, populations from north-central Oaxaca and Costa Rica each likely represent an undescribed species.