Population structure dictates the evolution of each population, and thus, the species as a whole. Incorporating spatial variables with population genetic statistics allows for greater discovery beyond traditional population genetics alone and can inform management decisions. The understanding of population structure in Hessian fly, Mayetiola destructor (Say), a pest of wheat, has been limited in the past. We scored 14 microsatellite loci from 12 collections of Hessian fly in the southeastern United States. Through Bayesian clustering analysis, we found two major populations of Hessian fly covering the entire southeastern United States. We evaluated correlations between agriculturally significant spatial variables and population genetic differentiation to test if genetic structure has an ecological component in a wheat agro-ecosystem. Our results suggest the total amount of alternative host plants in the county may be driving some genetic differentiation. Although planting date may also be influential, geographic distance, mean annual temperature, and harvested wheat for grain do not seem to be contributing factors. The ecological or spatial component to population structure, however, may be minimal compared to factors such as genetic drift.