Central to the process of speciation is understanding mate choice and its consequence, the evolution of reproductive isolation. The coordination of signal and response is essential to the evolution of divergent mating systems, but insights into the genetic processes that allow such coevolution to take place are limited. The two pheromone strains of the European corn borer (ECB) moth (Ostrinia nubilalis) allow for the study of a signal/response system, female production of pheromone, and male behavioral response. This study utilizes males collected from traps in New York State baited with either of the two pheromone blends and analyzes their genotypes at pgFAR, the gene responsible for divergent female pheromone production. ECB strains also differ in post-diapause development (PDD) time, which can contribute to temporal isolation in natural populations. Therefore, we also assay genotypes in a genomic region around Tpi associated with control of post-diapause development. Significant non-random associations are found between this region, pgFAR, and the type of trap in which a male was found. This study also assays field-collected females from New York, North Carolina, and Delaware for pheromone production, post-diapause development, and Tpi gene genealogies. Whereas populations in New York and North Carolina display the expected association between all three characters, the association between Tpi and pheromone production is disrupted in Delaware.