The Cerulean Warbler (Setophaga cerulea) is one of the most rapidly declining warblers in North America. Our previous genetic work suggested that this migratory songbird has no significant population genetic structure in the northern and western parts of its breeding range, and for conservation purposes we assigned all sampled populations to a single genetic management unit. Here, we expand this work to include the entire breeding range of the Cerulean Warbler, given recent evidence for morphological and ecological differentiation between the northern and southern sections of that range. We assayed variation in four microsatellite loci and an 841-base-pair fragment of the mitochondrial control region, finding support for low but significant population-genetic structure in the mitochondrial marker. Estimates of population-genetic structure for pairs of sampling locations did not detect a clear geographic pattern of differentiation, and a hierarchical AMOVA did not reveal significant structure between northern and southern locations. These findings, together with previously published evidence for high rates of contemporary dispersal among breeding locations, may support the hypothesis of a long history of gene flow among ecologically distinct Cerulean Warbler populations or may suggest that more recent anthropogenic dispersal has homogenized the genetic signature of differentiation that may have existed in pre-settlement populations.