Aedes albopictus and Aedes aegypti are the two main worldwide arbovirus vectors that have experienced invasion phases. Aedes aegypti is a pantropical species that spread centuries ago whereas Ae. albopictus started the main wave of invasion in the 1980s. Both species have been at various times on the different islands in Southwestern Indian Ocean (SWIO). This area provides an opportunity to examine the extent to which mosquitoes colonization patterns are influenced by different introductory events likely linked with human settlement and migration between the islands. To explore this hypothesis, we propose a CO1-based phylogeny using a large sampling of fresh Ae. albopictus, Ae. aegypti, and Ae. mascarensis, and 50-year-old dry specimens originating from different Indian Ocean islands. Our data allow us to hypothesize the existence of at least two waves of invasion for Ae. albopictus in the islands of SWIO. The first one most likely occurred several centuries ago with establishments in Madagascar, Mauritius and Reunion Island. The other one that appears to currently still on-going, reached almost all the islands of SWIO during the 1990s or later. The low genetic diversity found between the ancient invasive strain and the contemporary one, indicates with great certainty that Ae. albopictus is not indigenous to the islands of SWIO. Recently, in Madagascar, an invasive lineage of Ae. albopictus has expanded all over the island while Ae. aegypti populations have declined in urban areas. Three clusters of Aedes aegypti have been observed, two fitting with the wild form Ae. aegypti formosus and the other one fitting with the more domestic form Ae. ae. aegypti. Sequence of Ae. mascarensis, endemic to Mauritius suggest that this species might belong to Ae. aegypti species and on this basis we propose to classify it as a sub species or form of Ae. aegypti species. Given the increase of human population flux on these islands, the occurrence of these vectors and their ability t