Biological invasions generally induce profound effects on the structure of resident communities. In Mayotte, where Aedes aegypti and Ae. lilii were already present, the recent introduction of Ae. albopictus raises public health concerns because it may affect the risk of arbovirus transmission. Entomological surveys were carried out in six locations on the island following a transect defined by a gradient from urban to rural habitats during a dry and a wet season. A total of 438 larval habitats containing Aedes spp. immature stages were surveyed. We evaluated the characteristics of larval habitats and analyzed the field distribution of Aedes spp. throughout Mayotte using generalized linear models. Artificial containers used for water storage were significantly more productive for Ae. albopictus immature stages than for Ae. aegypti ones. Most of natural larval habitats collected were colonized by Ae. aegypti, and it was also the most common Aedes species encountered in rural habitats. Conversely, Ae. albopictus greatly predominated in urban and suburban habitats and during the dry season. Ae. lilii was uncommon and occurred preferentially in leaf axillae and dead leaves on the ground. Ae. albopictus has rapidly colonized the inhabited areas of Mayotte. A displacement of Ae. aegypti populations by Ae. albopictus populations in urban areas might be happening. The increasing urbanization seems to greatly favor the presence of the invasive species. Thus, arbovirus surveillance programs should focus, as a priority, on areas where this vector is present because of a higher risk of emergence of an epidemic source of arboviruses.