Across eastern North America, glacial cycles of the Pleistocene drove episodic latitudinal range shifts by temperate species. Isolation of populations within low-latitude refugia during glacial maxima was enhanced by physiographic barriers, leading to patterns of phylogeographic differentiation that are shared across diverse taxa. Postglacial population expansion created opportunities for differentiated lineages to come into contact, with various potential population-genetic outcomes. Northern short-tailed shrews (Blarina brevicauda) exhibit three mitochondrial phylogroups that probably originated via glacial-age range restriction and isolation. We investigate the history of postglacial expansion and interlineage contact between historically isolated regional populations of B. brevicauda. Morphological differences between skulls of shrews representing a Western lineage and those representing Central and Eastern lineages are consistent with past subspecies delineations. However, we demonstrate broad range overlap between neighboring phylogroups across the Upper Peninsula and Lower Peninsula in Michigan. Further, incongruence between phylogroup association and morphology among individuals in Upper Peninsula populations suggests that genetic admixture between shrews representing the Western and Central groups has occurred in the past and may be ongoing. We show that across most cranial measurements, shrews within the contact zone are morphologically most similar to the Central group regardless of mitochondrial identity, but one measurement in these contact zone shrews (depth of skull) is more similar to that seen in the Western group. These results suggest that hybridization between historically isolated populations has resulted in the origin of a novel skull phenotype that is proportionally deeper, narrower, and shorter than those seen in core Western and Central populations.