Preble's meadow jumping mouse (Zapus hudsonius preblei), a federally listed threatened subspecies, and the western jumping mouse (Zapus princeps princeps) typically occur parapatrically but in some areas may be syntopic. Field differentiation between the taxa is difficult so we investigated the use of cranial characteristics as a basis for identification. We developed a discriminant function conducted on the means of repeated measurements to distinguish between the taxa from an initial sample of 105 specimens (n = 71 Z. p. princeps and n = 34 Z. h. preblei). We found that measurement error can contribute significantly to erroneous reclassification of specimens when only a single measurement set is used. Use of only presence or absence of the anterior median toothfold of M3 is not a reliable method for distinguishing between the subspecies. We used the discriminant function to identify 8 of 16 specimens collected in southeastern Wyoming as Z. h. preblei.