Hessian fly is a wheat crop pest in the United States creating millions of dollars of crop losses each year. The primary means of controlling this insect pest is through the use of resistant cultivars. Over the years, this practice has led to Hessian flies containing genes for virulence. Additionally, other characteristics about Mayetiola destructor biology are likely to reduce gene flow between populations, however, virulence genes continue to spread. Knowledge of the population structure is important for monitoring the effects of any insect targeted control strategy, including the spread of virulence to deployed resistance genes in wheat, yet the population structure of this insect remains poorly understood. Microsatellite markers were used to identify population dynamics of the Hessian fly from the Southeastern United States. Levels of variation within and between populations are examined and the possible implications for this region are explored.