We investigated the genetic population structure of the Black-throated Blue Warbler (Dendroica caerulescens), a Nearctic-Neotropic migrant passerine that breeds in cool mixed deciduous-coniferous forests in eastern North America. A cline in plumage color in breeding populations in the central Appalachian Mountains suggests either a contact zone between two formerly allopatric populations or the presence of a strong contemporary selection gradient. Analysis of 333 base pairs of the mitochondrial control region from 287 individuals sampled from 14 populations revealed relatively high haplotype diversity, low nucleotide diversity, and limited but significant phylogeographic structure across the breeding range (analysis of molecular variance [AMOVA], variation among populations = 2.7%; P < 0.01) and between northern and southern population groups (AMOVA, variation among groups = 2.9%; P < 0.01). Genetic differentiation among populations did not conform to an isolation-by-distance model. Nucleotide diversity was generally highest in the central Appalachians and lower in geographically peripheral populations. Populations from the northwestern periphery of the breeding range in Michigan had the lowest haplotype diversity and were genetically distinct from populations in the southern Appalachians. The star-shaped haplotype network, extensive sharing of common haplotypes among populations, and the haphazard distribution of rare haplotypes are most likely attributable to the combined effects of postglacial expansion from a single refugium (12,000-84,000 years ago) and long-distance dispersal events. The existence of a cline in plumage color, in the face of inferred recent gene flow, suggests that a strong selection gradient is operating, perhaps related to the migratory divide postulated from stable-isotope data.