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Aedes aegyptidevelop in aquatic habitats in which mosquito larvae are exposed to physicochemical elements and microorganisms that may influence their life cycle and their ability to transmit arboviruses. Little is known about the natural bacterial communities associated withA. aegyptior their relation to the biotic and abiotic characteristics of their aquatic habitats. We characterized the physicochemical properties and bacterial microbiota ofA. aegyptibreeding sites and larvae on Guadeloupe and in French Guiana. In addition, we explored whether geographic location, the type of breeding site and physicochemical parameters influenced the microbiota associated with this mosquito species. We used large-scale 16S rRNA gene sequencing of 160 breeding sites and 147 pools ofA. aegyptilarvae and recorded 12 physicochemical parameters at the sampled breeding sites. Ordination plots and multiple linear regression were used to assess the influence of environmental factors on the bacterial microbiota of water and larvae. We found territory-specific differences in physicochemical properties (dissolved oxygen, conductivity) and the composition of bacterial communities inA. aegyptibreeding sites that influenced the relative abundance of several bacteria genera (e.g.,Methylobacterium,Roseoccocus) on the corresponding larvae. A significant fraction of the bacterial communities identified on larvae, dominated byHerbiconiuxandMicrovirgagenera, were consistently enriched in mosquitoes regardless the location. In conclusion, territory-specific differences observed in the biotic and abiotic properties ofA. aegyptibreeding sites raise concern about the impact of these changes on pathogen transmission by differentA. aegyptipopulations.