A significant challenge to population genetic studies of the dengue vector, Aedes aegypti, has been the lack of polymorphic microsatellite loci. In an effort to develop useful markers, we evaluated the genetic variation at 17 microsatellite loci identified in the A. aegypti genome. Nine loci with at least five alleles were identified in field-collected specimens from Thailand. An additional two loci carried five alleles if samples from an A. aegypti laboratory colony were included. Our results greatly increase the number of highly variable markers available for the study of the genetics and the population structure of this medically important species.