Prairie (Microtus ochrogaster) and meadow (M. pennsylvanicus) voles are morphologically very similar species of rodents that are often found sympatrically. To assess the reliability of morphological characters typically used to differentiate between these two species, we compared the concordance of species identification based on morphological characteristics with identifications based on a species-specific difference within the avpr1a gene. We found that intraspecific variation in morphological characteristics resulted in erroneous or ambiguous species identification in the field (generally ≤5%) as well as for preserved specimens (up to ∼45%). Our data suggests that genotyping putative M. ochrogaster and M. pennsylvanicus at their avpr1a locus may be warranted for some individuals to ensure accurate species identification.