Bemisia tabaci (Hemiptera: Aleyrodidae) is a haplo-diploid species of sap-feeding insect belonging to the group of insects commonly known as whiteflies. From earlier analyses of mitochondrial and ribosomal markers it has been concluded that in the Asia–Pacific region there were three major indigenous races as well as a large collection of genotypes with no clear association with any race. This new study uses 15 microsatellite loci and demonstrates that the indigenous Asia–Pacific genotypes can be split into six genetic populations with little or no gene flow between them. These bare only superficial similarity to the mitochondrial and ribosomal defined races. Moreover, four of the six can be further split into two subpopulations that again show little evidence gene flow between them. While the patterns reflect a strong geographical structure, physical barriers alone cannot explain all the observed structure. Differential host-plant utilization explained some of the substructure, but could not explain the overall structure. The roles of mating interference and Wolbachia in developing the genetic structure are considered. The lack of gene flow between genetic populations and some subpopulations further suggests that the barriers were either sufficiently impermeable to immigration or that reproductive isolation and competitive interactions were sufficiently strong to prevent gene flow. If the latter is the case, it suggests that there may be as many as 10 morphologically indistinguishable species indigenous to the Asia–Pacific region.