Acorn Woodpecker (Melanerpes formicivorus) populations were sampled to evaluate geographic patterns of differentiation and connectivity across the species' range. We observed patterns of differentiation generally coincident with geographic patterns in plumage patterns with distinct subpopulations in Baja California Sur, northern Central America, southern Central America, and mainland Mexico north into the southwestern United States. We confirmed the existence of geographic genetic structuring of populations of this species, although shared haplotypes between Baja California Sur and mainland Mexico suggest that lineage sorting is not yet complete. The process of geographic differentiation and speciation is likely still underway in this group.