We used sequences of the mitochondrial ND2 gene, the nuclear TGFB-2 intron-5, and differences in plumage pattern to assay geographic variation in the Red-bellied Woodpecker (Melanerpes carolinus). Ten population samples from throughout its range indicated that ∼23% of the mitochondrial genetic variation was distributed among populations, largely due to the occurrence of a clade of haplotypes restricted to the Florida peninsula with a local frequency of 82%. In a hierarchical analysis, 37% of the mtDNA genetic variance was distributed between the Florida peninsula and elsewhere. A strong signal of population growth was detected in the non-peninsular portion of the range. Otherwise, geographic variation in haplotype frequencies was minor, with no evidence of isolation-by-distance. Nuclear intron data showed little variation among populations (Fst = 0.007). These results suggest recent secondary contact of 2 differentiated taxa following expansion from allopatric Pleistocene refugia. We modeled the transition in haplotype frequencies along the Florida peninsula as a zone of neutral introgression; the estimated width of that zone was 435 km, and its center was near present day Ocala. Variation in plumage pattern along the peninsula previously had been used to describe a subspecific taxon, M. c. perplexus. We used variation in the forehead pattern of adult males from along the east coast of the United States to model this phenotypic transition; the zone had an estimated width of >2,500 km and an approximate center in the Florida Keys. Taken together, the geographic patterns in mtDNA and plumage variation suggest the populations of Red-bellied Woodpeckers on the Florida peninsula differentiated from those elsewhere during isolation; they are now in secondary contact in a well-known suture zone and represent 2 phylogenetic species connected by wide molecular and morphological zones of introgression.