To slow the resistance evolution of the European corn borer (ECB) to Cry proteins expressed in transgenic Bacillus thuringensis (Bt) corn, the United States Environmental Protection Agency (EPA) has adopted an insect resistance management (IRM) plan that relies on a “high dose/refuge” strategy. However, this IRM plan does not consider possible ecological differences between the two ECB pheromone races (E and Z). Using carbon isotope analysis, we found that unstructured (non-corn) refuges contribute more to E race (18%) than to Z race (4%) populations of ECB in upstate New York (USA). Furthermore, feeding on non-corn hosts is associated with decreased body mass and reduced fecundity. We also show that the geographic range of E-race ECB is restricted within the range of the Z race and that E-race ECB are increasingly dominant in regions with increasing non-corn habitat. While the proportion of E-race ECB developing in unstructured refuges is higher than previously assumed, low rates of unstructured refuge use by the Z race, evidence for reduced fecundity when reared on non-corn hosts, and complete sympatry within the E race range all argue against a relaxation of current IRM refuge standards in corn based on alternative-host use. We also discuss implications of this research for integrated pest management in vegetables and IRM in Bt cotton.