We studied spatial and temporal variation in 20-23 Aedes aegypti samples collected in Phnom Penh and its suburbs to estimate the population genetic structure using allozymes and the susceptibility to a dengue-2 virus. Based on seven allozyme systems, we detected low levels of genetic exchanges (i.e. high, significant F(ST) values) between populations collected in the city centre, and different patterns of genetic structure for samples collected in the suburbs, depending on the type of environment and the date of collection. In the southern suburbs and the Chroy Chang Var Peninsula, differentiation became highly significant at the end of the dry season, whereas the opposite situation was observed for collections from the northern suburbs. Vector competence assessed by oral infections with a dengue-2 virus was lower for samples collected in the city centre than in the suburbs. A significant decrease of dengue susceptibility was observed in populations during the dry season. This study allows a model of Ae. aegypti population functioning in Phnom Penh to be suggested. Dynamics of dengue virus diffusion depend on the population genetic structure of the vector and its evolution over space and time.