Species in recent, rapid radiations can be difficult to distinguish from one another due to incomplete sorting of traits, insufficient time for novel morphologies to evolve, and elevated rates of hybridization and gene flow. The vole genus Microtus (58 spp.) is one such system where all three factors are likely at play. In the central United States, the prairie vole, Microtus ochrogaster, and the eastern meadow vole, M. pennsylvanicus, occur in sympatry and can be distinguished on the basis of molar cusp patterns but are known to be exceptionally difficult to distinguish using external morphological characters. Using a combination of morphometrics, pelage color analyses, and phylogenetics, we explored which traits are most effective for species identification and whether these same traits can be used to identify the subspecies M. o. ohionensis. While we were able to identify six traits that differed significantly between M. ochrogaster and M. pennsylvanicus, we also found substantial measurement overlap which limits the utility of these traits for species identification. The subspecies M. o. ohionensis was particularly difficult to distinguish from M. p. pennsylvanicus, and we did not find any evidence that this subspecies forms a distinct genetic clade. Furthermore, the full species M. ochrogaster and M. pennsylvanicus did not form reciprocal clades in phylogenetic analyses. We discuss several possible reasons for these patterns, including unrecognized variation in molar cusp patterns and/or localized hybridization. Overall, our results provide useful information that will aid in the identification of these species and subspecies in the future, and provides a case study of how genetics, morphometrics, and fur color analyses can be used to disentangle signatures of evolutionary history and hybridization.