The maritime shrew, Sorex maritimensis, is a Canadian endemic species with a limited distribution in two provinces in eastern Canada. Phylogeographic analysis of mitochondrial DNA control region and cytochrome b sequences revealed two clades, one found in New Brunswick and the other primarily in Nova Scotia, Canada. We propose that these clades have come back into secondary contact following the Wisconsin glaciation via wetlands on the narrow Isthmus of Chigneto that connects these provinces. Despite evidence of an historic separation of maritime shrew subpopulations in Nova Scotia and New Brunswick, we conclude that shrews in these two regions should be considered a single evolutionary significant unit but separate, semi-isolated management units that should be recognized as such for conservation purposes. The susceptibility of this stenotopic species with limited dispersal capabilities raises concerns about its long-term persistence if climate-change induced habitat fragmentation increases. Maintenance of contiguous wetland habitats is needed to ensure connectivity and gene flow among populations of the maritime shrew.