The mosquito, Aedes albopictus, has recently become established in a number of cities throughout the United States. An initial survey of allozyme and genotypic frequencies in U.S. populations (Black et al., 1988) revealed an extensive amount of local differentiation of populations and suggested that much genetic drift may have accompanied colonization. A study of gene flow was initiated in native habitats of Ae. albopictus in Malaysia to determine if the result observed in the U.S. was a consequence of colonization or simply followed the natural breeding structure of the species. Allelic and genotypic frequencies were monitored at ten enzymatic loci in 11 populations from peninsular Malaysia and Borneo. Multiple populations were sampled within the districts of Kuala Lumpur and Kuala Trengganu. Peninsular Malaysian and Borneo populations were strongly genetically differentiated. Allele frequencies were significantly different among and within districts in both regions. Variance in allele frequencies among all collections was partitioned into the variance among regions, districts within regions and collections within districts. Almost all of the variance within regions was attributable to local differentiation suggesting that genetic drift is an important component of the natural breeding structure of this species. This indicates that the large amounts of local differentiation found in U.S. populations was not a consequence of recent colonization.