We used mitochondrial DNA sequences to investigate the phylogenetic relationship of Rana subaquavocalis and Rana chiricahuensis. We sequenced 1344 base pairs of the mitochondrial control region from 39 samples of R. subaquavocalis and 53 samples of R. chiricahuensis from localities throughout their Arizona range. In maximum-likelihood analysis, R. subaquavocalis samples were on a short branch within the southern Arizona clade of R. chiricahuensis. We also found two distinct lineages of R. chiricahuensis, one on the Mogollon Rim of central Arizona and one in southern Arizona. Our results are consistent with the hypothesis that R. chiricahuensis and R. subaquavocalis are conspecific.