In Wisconsin white-footed mice (Peromyscus leucopus noveboracensis) and woodland deer mice (P. maniculatus gracilis) are difficult to distinguish. Recent climatic trends have facilitated encroachment of P. leucopus north into the range of P. maniculatus, necessitating unambiguous species identification as researchers begin to untangle the ecological implications of such community changes. Cranial and external measurements have been used by previous investigators to differentiate these species in other regions. However, because large geographic morphological variation occurs and most previous studies used measurements from dead specimens, definitive morphological characteristics need to be identified that can quickly and effectively classify live Wisconsin Peromyscus in the field. During the summer of 2010, we collected tissue samples and measured ear length, tail length, hindfoot length, and body weight of 84 P. maniculatus and 293 P. leucopus live-trapped in six Wisconsin counties. We used mDNA analysis to identify species. We developed discriminate function analysis (DFA) equations to identify characteristics that best distinguished species. Ear length correctly classified 97.9% of the samples with all but one P. leucopus <17 mm and all but seven P. maniculatus ≥17 mm. By adding body weight to the function, we were able to achieve 99.2% classification accuracy and with the addition of tail length were able to achieve 99.5% accuracy.