Prairie (Microtus ochrogaster) and woodland (Microtus pinetorum) voles, which exhibit distinctly different ecological preferences (grassland versus forest), commonly co-occur in paleontological deposits in eastern North America. Despite their ecological differences, their molar morphology is similar. Assuming that those ecologic differences occurred in the past, differentiation of these two taxa is important for paleoenvironmental reconstruction. A sample of 51 lower first molars from living populations were viewed via scanning electron microscope to qualify and quantify schmelzmuster (enamel microstructure) to species-specific standards applicable to the fossil record. The most obvious differences between schmelzmuster of the two taxa are the relatively thicker bands of radial enamel on the leading edges of triangles of M. ochrogaster, as well as the consistent retention of tangential or primitive tangential enamel on the trailing edges and posterior enamel band of the posterior loop of M. pinetorum. Discriminant analysis of landmark data from the same 51 specimens established morphological boundaries for these taxa and successfully separated the recent m1s of M. ochrogaster from those of M. pinetorum.To test identification confidence from previous work, and to add an independent means of identification for future work (at any site), both techniques were applied to a sample of three-closed triangle (“M. ochrogaster” type) m1s from the late Pleistocene Wapsipinicon Local Fauna of Jones County, Iowa. Identifications of the specimens from the Wapsipinicon l.f. based on schmelzmuster and morphometric analysis are consistent with those reached using traditional morphology. Such methods serve as independent “check” of traditional (qualitative) identification, highlight new species-level characters, and quantify previously described features, for discrimination of these taxa.