Sorex cinereus (masked shrew) and Sorex fumeus (smoky shrew) are syntopic species co-occurring in relict fragments of spruce–fir habitat on southern Appalachian mountaintops. We conducted phylogenetic and population genetic analyses of 20 high-elevation Sorex populations in 8 distinct boreal islands. Partial mitochondrial DNA sequences (cytochrome b and D-loop) were compared with amplified fragment length polymorphism markers obtained by restriction of whole genomic DNA. The 2 species, though similar in morphology and ecological niche, have dissimilar phylogeographic patterns. S. cinereus, despite its more limited present-day southern Appalachian range, exhibits markedly less population structure than S. fumeus. What structure is present among masked shrew populations is randomized geographically, in contrast to a distinct association between genetic partitioning and geographic location among smoky shrew populations. Disparity in post-Pleistocene population densities of these species might be implicated in the discrepant patterns of phylogeographic structuring evident in their genomes as a result of historical vicariance. Although the metapopulations of both species exhibit genetic signatures consistent with continuous historical expansion, we believe that a localized catastrophic event induced a severe genetic bottleneck in Sorex populations at Whitetop Mountain, Virginia. This study contributes to a better understanding of the repercussions of boreal habitat fragmentation on the population dynamics and genetic diversity of associated vertebrate species.