Microsatellites were used as markers for a study of the population structure of Anopheles funestus on Madagascar and Comoros. Mosquitoes were collected in four different localities on Madagascar and one on Comoros. There was a significant genetic differentiation between all samples from Madagascar and that from Comoros (P<0.05). With respect to the Madagascar mosquito samples, it was found that there were no significant genetic differences between samples that were collected at the east coast, and in the highlands, respectively. By contrast, the west coast sample exhibited significant genetic differences (with regard to all Madagascar samples). The results are discussed with respect to population distribution and migration of A. funestus from mainland Africa and the islands east of the mainland.
