We analysed the population genetic structure and differentiation regarding vector competence for a dengue virus of 15 Aedes aegypti samples collected from Chiang Mai in northern Thailand. Based on polymorphism of 10 isoenzyme loci, genetic differentiation was confirmed among samples collected in different subdistricts (high FST values and P < 0.05). Based on infection rate for a dengue 2 virus, susceptibilities were similar in mosquitoes collected in San Nuea subdistrict and in Choeng Doi subdistrict, and were heterogeneous in populations sampled in other subdistricts. These findings are discussed and related to insecticide treatments.