Males of the E and Z strains of the European corn borer Ostrinia nubilalis (Lepidoptera: Crambidae) are attracted to different blends of the same pheromone components. The difference in male behavioral response is controlled by the sex‐linked locus Resp. The two types of males have identical neuroanatomy but their physiological specificity is reversed, suggesting that variation at the periphery results in behavioral change. Differences in the olfactory receptors (ORs) could explain the strain‐specific antennal response and blend preference. Gene genealogies can provide insights into the processes involved in speciation and allow delineation of genome regions that contribute to reproductive barriers. We used intronic DNA sequences from five OR‐encoding genes to investigate whether they exhibit fixed differences between strains and therefore might contribute to reproductive isolation. Although two genealogies revealed shared polymorphism, molecular polymorphism at three genes revealed nearly fixed differences between strains. These three OR genes map to the sex chromosome, but our data indicate that the distance between Resp and the ORs is >20 cM, making it unlikely that variation in pheromone‐sensitive OR genes is directly responsible for the difference in behavioral response. However, differences in male antennal response may have their origin in the selection of strain‐specific alleles.