Hybrid zones between recently diverged taxa are natural laboratories for speciation research, allowing us to determine whether there is reproductive isolation between divergent forms and the causes of that isolation. We present a study of a classic avian hybrid zone in North America between two subspecies of the yellow-rumped warbler (Dendroica coronata). Although previous work has shown very little differentiation in mitochondrial DNA across this hybrid zone, we identified two nuclear loci (one sex-linked and one autosomal) that show fixed differences across the hybrid zone, in a close concordance with patterns of plumage variation. Temporal stability and limited width of the hybrid zone, along with substantial linkage disequilibrium between these two diagnostic markers in the center of the zone, indicate that there is moderate reproductive isolation between these populations, with an estimated strength of selection maintaining the zone of 18%. Pairing data indicate that assortative mating is either very weak or absent, suggesting that this reproductive isolation is largely due to postmating barriers. Thus, despite extensive hybridization the two forms are distinct evolutionary groups carrying genes for divergent adaptive peaks, and this situation appears relatively stable.