Isoenzyme genetic differentiation of Aedes polynesiensis mosquitoes in Raiatea island, French Polynesia, was evaluated by two models of population structure based on seven gene-enzyme systems: Ak, Est, Got, Gpi, Hk, Mdh and Pgm. The ecological model tested whether genetic differentiation is congruent with habitat differences. The isolation model evaluated whether genetic differentiation is proportional to geographical distribution. The ecological model found no significant differentiation between populations of Ae.polynesiensis from beach and forest ecotopes, whereas the isolation model was consistent with the data. However, incipient speciation is opposed by the source-sink system of population dynamics in such small neighbouring islands, where Ae.polynensiensis extinction is readily followed by reinvasion causing considerable gene flow between island populations.