The Aedes aegypti mosquito is the main vector for dengue (DENV) and Zika (ZIKV). It becomes urgent to develop new tools to reduce the transmission of these viruses to humans by the mosquito. One promising area concerns bacteria associated with mosquito vectors: the bacterial microbiota. The natural variability in the biotic and abiotic breeding site properties may shape the microbiota of mosquitoes, and indirectly influence phenotypic traits related to their ability to transmit viruses. We showed that Ae. aegypti larvae from Guadeloupe and French Guiana have their own microbiota, influenced by the physico-chemical properties and bacterial communities from the water of their respective breeding sites. We then showed that Ae. aegypti from Guadeloupe is capable of transmitting DENV and different strains of ZIKV with contrasted efficiencies depending on the viral strain. Next, we exposed Ae. aegypti larvae to contrasting bacterial microbiota in order to evaluate their impact on the bacterial microbiota of adult, their vector competence and their survival. We found significant differences in the transmission of ZIKV between mosquitoes from different breeding conditions. We observed differences in survival, driven by the microbiota of breeding sites and the infectious bloodmeal. Taken together, our results show that differences on breeding sites microbiota can impact vector competence and survival of adult mosquitoes. This thesis work improves knowledge of the dynamics of bacterial communities associated with Ae. aegypti and its impact on the vectorial competence of this vector, with the goal of identifying candidate bacteria to reduce virus transmission by Ae. aegypti.