Birds of the Northern Hemisphere often harbour the genetic signature of postglaciation expansion but analyses identifying the location of refugia and the directionality of expansions are rare. Here we explore the evolutionary history of yellow warbler lineages, focusing on how these lineages recolonized their current range. We genotyped samples from 696 yellow warblers via direct sequencing of a 333-bp control region I mitochondrial DNA fragment or lineage-specific genotyping. Phylogenetic analysis revealed two monophyletic clades: a highly migratory group including previously identified eastern and western lineages and a less migratory group including a lineage consisting of tropical residents and a new ‘southern’ lineage localized in southwest United States. We then modelled the expansion of the eastern and western lineages, identified the location of potential refugia and assessed the importance of migration as a historical factor promoting gene flow. The expansion of the eastern lineage proceeded from a main refugia in the eastern United States, with possible contribution of an additional local refugia. In the western lineage, the expansion proceeded from a single refugia possibly located in western United States. Because two lineages overlapped to varying degrees in central North America, we suggest that the Canadian Prairies offered a bridge of riparian habitats where the lineages met after glacier retreat, while the US Central Great Plains acted as a barrier that limited secondary contact. Finally, gene flow was more important along the north–south axis of migration than away from it, suggesting spring migration played a role in the dispersal of lineages.