The population structure of the Polynesian mosquito Aedes polynesiensis was investigated using electrophoretic data from two polymorphic protein loci. Considerable differentiation was observed both within and between islands in different archipelagos (Society, Tuamotu, Austral). Gene flow evaluated by F-st estimates was independent of geographic distance between islands but related to commercial traffic intensity. The results are discussed in view of recent findings on the variability of susceptibility to insecticides and of suitability as a vector for the nematode Wuchereria bancrofti.