We used morphometrics, plumage color, and mitochondrial DNA to reconstruct the phylogeography of the Plain Wren (Cantorchilus modestus), an abundant bird species of low to middle elevations throughout Central America. Sampling the full geographic range of C. modestus, we uncovered significant phenotypic structure in size, shape, and plumage color that mirrored deep genetic divergences in mitochondrial DNA. This structure was mostly concordant with the 3 most broadly recognized subspecies of Plain Wren (C. m. modestus, C .m. zeledoni, and C. m. elutus), but a potentially undescribed taxon exists in the highlands of Central Belize. We also found evidence of a cryptic phylogeographic break on the Pacific Slope of Costa Rica, between the southernmost populations and the widespread northern populations. This latter discovery likely represents a significant expansion of the known range of the traditionally Panamanian subspecies C. m. elutus, corresponding to a transition between major ecoregions. Topology tests suggested that northern populations of the nominate taxon likely dispersed south into Lower Central America, with subsequent isolation and diversification. We also explored the possible role of adaptation in the phenotypic divergence of the “Canebrake Wren” (C. m. zeledoni) as a result of isolation in the more humid environments of the Caribbean Slope. Our data and analyses suggest that the Plain Wren may consist of multiple biological species that have been diverging since geophysical upheavals in the lower half of Central America approximately 2–3 mya.