Female European corn borer, Ostrinia nubilalis, produce and males respond to sex pheromone blends with either E- or Z-Δ11-tetradecenyl acetate as the major component. E- and Z-race populations are sympatric in the Eastern United States, Southeastern Canada, and the Mediterranean region of Europe. The E- and Z-pheromone races of O. nubilalis are models for incipient species formation, but hybridization frequencies within natural populations remain obscure due to lack of a high-throughput phenotyping method. Lassance et al. previously identified a pheromone gland-expressed fatty-acyl reductase gene (pgfar) that controls the ratio of Δ11-tetradecenyl acetate stereoisomers. We identified three single nucleotide polymorphism (SNP) markers within pgfar that are differentially fixed between E- and Z-race females, and that are ≥98.2% correlated with female pheromone ratios measured by gas chromatography. Genotypic data from locations in the United States demonstrated that pgfar-z alleles were fixed within historically allopatric Z-pheromone race populations in the Midwest, and that hybrid frequency ranged from 0.00 to 0.42 within 11 sympatric sites where the two races co-occur in the Eastern United States (mean hybridization frequency or heterozygosity (HO) = 0.226 ± 0.279). Estimates of hybridization between the E- and Z-races are important for understanding the dynamics involved in maintaining race integrity, and are consistent with previous estimates of low levels of genetic divergence between E- and Z-races and the presence of weak prezygotic mating barriers.