Endoparasitoids of herbivorous lepidopterans have intimate relationships with their host species as well as the plant on which their host develops. Characteristics of both hosts and plants can affect parasitoid success in tri-trophic systems and thus, drive diversification. Genetic differentiation was estimated for Cotesia congregata (Say) collected from two distinct host-plant complexes, Manduca sexta L. on tobacco (Nicotiana tabacum L.) and Ceratomia catalpae, (Haworth) on catalpa (Catalpa bignonioides Walker), in the mid-Atlantic region of North America using seven microsatellite loci and the mitochondrial COI locus. Microsatellite allele frequencies were differentiated based on host-plant complex, and COI haplotypes from individuals on the same host-plant were identical despite geographic distances between catalpa sites of up to 830 km and distances between tobacco sites of up to 294 km. Results indicate genetic differentiation of subpopulations of C. congregata based on host-plant complex and not geographic distance, and were designated as host races. Cotesia congregata is a gregarious parasitoid, meaning that many individuals develop in a single host larva. Superparasitism, or repeated egg-laying events in the same host larva, is likely to occur in gregarious species. Brood size was not a good predictor of superparasitism in C. congregata, but within-brood male allele diversity indicates either superparasitism or multiple mating by female wasps.