The Rufous-naped Wren (Campylorhynchus rufinucha) is a sedentary, morphologically variable species distributed in the dry forests of Mesoamerica. It ranges from Colima, Mexico, south to Costa Rica along the Pacific slope, with a disjunct population in central Veracruz. Populations of two forms on the Pacific slope intergrade in Chiapas, Mexico, apparently as a result of secondary contact. We sequenced a mitochondrial DNA (mtDNA) gene to explore phylogeographic patterns and hybridization. We found three divergent lineages, two geographically spanning the Isthmus of Tehuantepec and a disjunct Veracruz population. Analyses of molecular variation and φ; statistics are consistent with genetically distinct populations. Morphological and behavioral evidence from other studies is consistent with the existence of these three independent evolutionary lineages. However, the geographic distribution of haplotypes suggests mtDNA introgression east of the isthmus. Our data suggest that this secondary contact could be explained by population expansions. We recommend recognizing three species, two of which hybridize in a narrow contact zone.