The extensive use of insecticides in the attempt to reduce pest population densities, and the growing concern about their impact on non-target species, human health and the environment make the study of measures aimed at rationalizing the use of chemicals a fundamental goal of the applied sciences. To this aim, the knowledge of the patterns of population connectivity is of great relevance. These data can allow us to gain insight into the appropriate geographic scale for control programmes as well as understand how far and fast a potential resistance allele may spread. Population genetic structure and diversity was investigated, by means of both nuclear and mitochondrial markers, in two mosquito species of great economic and medical interest for our country: Ochlerotatus caspius and Aedes albopictus. The relavence of these data to assess the patterns of connectivity among populations and to improve control planning is discussed.