Aedes aegypti is the main vector of dengue viruses responsible for dengue hemorrhagic fever, which has become a major public health concern in tropical countries. Because vaccines are still under development, dengue prevention depends entirely on vector control. Knowledge of gene dispersal patterns is required to develop efficient vector control strategies. Here we report the use of amplified fragment length polymorphism (AFLP) to infer the genetic structure of Ae. aegypti populations at a local levels (Phnom Penh, Cambodia). The amount of variation and patterns of gene flow detected are compared with those obtained with two other more widely used markers, isoenzymes and microsatellites. The pattern of differentiation depicted by AFLP data were confirmed by comparison of the F_st values of the three markers. Even though F_st values estimated with AFLP markers are three- to fivefold higher than those estimated with isoenzymes or microsatellites, these different markers reveal the same population structure. This technique is useful for population genetic studies of Ae. aegypti and is especially advantageous when few individuals specimens are available because of the ability to AFLP to simultaneously amplify large numbers of polymorphic DNA fragments.