The whitefly Bemisia tabaci is a pest vector of begomoviruses on crops worldwide. Bemisia tabaci is composed of a complex of cryptic species which barely interbreed. An exception is the Ms from the South West Indian Ocean (SWIO), which crosses in low proportions with the exotic B. The Ms, together with B and Q is part of the same phylogenetic clad. To infer the genetic structure, the geographical range and putative origin of this putative species, microsatellite data and mitochondrial DNA (cytochrome oxydase I) sequences were analysed on an extensive sample set, including all the islands of the region and samples from mainland Africa. Only B and Ms populations were detected across these islands. The exotic B was found only on the islands of Réunion and Mauritius, whereas the Ms is found on all the SWIO islands. Very high isolation by distance was found for the Ms populations between islands of the SWIO, suggesting a long period of presence in this region. Ms populations from mainland Africa had a higher COI diversity than the Ms of the SWIO islands. This diversity is correlated with size and geological ages of the SWIO islands. The population genetic data obtained are in accordance with an origin of Ms in Africa, followed by its expansion and evolution across the SWIO islands prior to human arrival, confirming the status of Ms as indigenous in the SWIO islands.