The Preble's meadow jumping mouse (Zapus hudsonius preblei) is listed as a threatened subspecies under the United States Endangered Species Act (US-ESA). The quantitative description of this subspecies was based on cranial measurements of only three adult specimens. It is one of twelve subspecies of Z. hudsonius and is a peripheral population at the western edge of its range. We tested the uniqueness of Z. h. preblei relative to other nearby subspecies of Z. hudsonius using a hypothesis testing approach and analyses of cranial morphometric, mtDNA sequence and nuclear microsatellite data obtained from museum specimens and archived tissues. Morphometric analysis of variance did not support the original description of Z. h. preblei as a subspecies. Principal component analysis of these data showed Z. h. preblei within the range of variation found in Z. h. campestris and Z. h. intermedius. Discriminant analysis correctly classified only 42% of Z. h. preblei skulls at jackknifed posterior probabilities >0.95 relative to Z. h. campestris. All mtDNA haplotypes found in Z. h. preblei were also found in Z. h. campestris. Simulation based estimates of current and historical gene flow (MDIV) revealed low, but non-zero, mtDNA gene flow among Z. h. preblei and several nearby subspecies. Analyses of five nuclear microsatellite loci using population pairwise FST, BAPS and STRUCTURE were consistent with morphometric and mtDNA results. These revealed low levels of genetic structure and evidence of recent gene flow and bottlenecks in Z. h. preblei. Due to a lack of clearly recognisable genetic, morphological, or adaptive differences, we synonymise Z. h. preblei and Z. h. intermedius with Z. h. campestris. We suggest that candidates for listing under the US-ESA, or similar biodiversity laws, be evaluated for genetic and/or morphological uniqueness to prevent the misallocation of resources to non-distinct taxa like Z. h. preblei.