In the absence of effective and affordable control strategies to block disease in the mammalian host, most control efforts utilize tsetse reduction methods. We are using population genetics to identify the historical and modern processes that account for the current level and distribution of genetic variation in tsetse. This information can help us to identify isolated populations that may be appropriate units for control. Before undertaking methods involving genetically modified insects or sterile males, it is important to predict the extent to which they are likely to interact with wild populations. This can help characterize the geographic scale on which local interactions between tsetse and trypanosomes may be influencing disease epidemiology. Our work focuses in Uganda and has yielded insight into linkages among populations of G. fuscipes, an important vector of human and animal trypanosomiasis. These data have the potential to help Ugandan control programs as they undertake fly eradication efforts.