The distribution of Aedes aegypti (L.) in Australia is currently restricted to northern Queensland, but it has been more extensive in the past. In this study, we evaluate the genetic structure of Ae. aegypti populations in Australia and Vietnam and consider genetic differentiation between mosquitoes from these areas and those from a population in Thailand. Six microsatellites and two exon primed intron crossing markers were used to assess isolation by distance across all populations and also within the Australian sample. Investigations of founder effects, amount of molecular variation between and within regions and comparison of F(ST) values among Australian and Vietnamese populations were made to assess the scale of movement ofAe. aegypti. Genetic control methods are under development for mosquito vector populations including the dengue vector Ae. aegypti. The success of these control methods will depend on the population structure of the target species including population size and rates of movement among populations. Releases of modified mosquitoes could target local populations that show a high degree of isolation from surrounding populations, potentially allowing new variants to become established in one region with eventual dispersal to other regions.