Studies of genetic variation across hybrid zones have demonstrated that the evolutionary dynamics within them are often complicated. Using DNA extracted from toe pads of 701 individuals collected by Sibley and Short (1964) about 50 years ago from across the Icterus bullockii—I. galbula hybrid zone, we calculated mitochondrial cline shape parameters and compared them with plumage-based inferences of the hybrid-zone structure. Genetic and hybrid index score dines, estimated from populations collected along the Platte River in Nebraska, were both concordant (equal widths) and coincident (same center). More generally, the proportion of I. bullockii haplotypes within a sampling locality was strongly and significantly correlated with mean hybrid index scores across Colorado, Kansas, Nebraska, Oklahoma, and South Dakota. The relatively narrow width of the mitochondrial cline (328 km) indicates selection against hybridization, which may be mediated through differences in either molt and migration schedules or thermoregulatory capabilities (or both) of the parental species. Our results provide the first robust historical genetic characterization of this avian hybrid zone, laying the foundation for more in-depth investigations of temporal patterns of gene flow and introgression.