Populations of the masked shrew (Sorex cinereus) and the prairie shrew (S. haydeni) occurring in sympatry in Alberta were compared genetically with each other and with populations of S. cinereus across Canada using protein electrophoresis of 33 loci. Despite distinct morphologic differences between S. cinereus and S. haydeni, in Alberta these taxa were less genetically differentiated (Ne's genetic distance, DN = 0.006; Rogers' genetic distance, DR = 0.047) than were conspecific populations of S. cinereus across Canada (DN = 0.019; DR = 0.058). Although there were no fixed allele differences among the populations sampled, there was a unique allele at a moderate frequency in S. haydeni (PEP-SB, 0.375). This may be indicative of no gene flow between these two taxa and thus they may be valid species. The genetic similarity of the masked and prairie shrews implies that S. cinereus is a paraphyletic taxon and suggests a recent divergence of these taxa, perhaps in the late Pleistocene or the early Holocene. Among populations of S. cinereus across Canada, the pattern of differentiation is consistent with a biogeographic model in which shrews re-colonized Canada from multiple refugia following the retreat of the Wisconsin glaciers.