Aedes aegypti, the mosquito responsible for transmitting dengue, has colonized many cities and towns throughout Arizona. Determining both the migration between, and the origin of, local Ae. aegypti populations is important for vector control and disease prevention purposes. Amplified fragment length polymorphism was used to infer geographic structure and local substructure, and effective migration rates (M, migrants per generation) between populations, and to determine genetic differentiation between populations (PhiPT). Three geographically and genetically differentiated groups of populations were identified. Population substructure was only detected in the border town of Nogales. Reliable estimates of M between regions ranged from 1.02 to 3.41 and between cities within regions from 1.66 to 4.44. In general, pairwise PhiPT were lowest between cities within regions. The observed patterns of genetic differentiation suggest infrequent migration between populations and are compatible with the idea of human transport facilitating dispersal between regions.