Black-capped vireos (Vireo atricapilla), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation (F(ST) = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black-capped vireos are capable of large-scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.