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Abstract Aedes aegypti mosquitoes are the main vector of pathogens like dengue virus and chikungunya virus. The immature life stages of mosquitoes share the same habitat with a variety of microorganisms in aquatic environments. To better understand the microbial diversity in field-derived Ae. aegypti , we analysed simultaneously collected larvae, pupae, and freshly emerged adults from Burkina Faso together with their breeding water via 16S rRNA gene sequencing. We observed a decrease in bacterial diversity and load across the mosquito life stages. At the phylum level, a strong increase in relative abundance of Proteobacteria was found along the mosquito stages. The same 40 amplicon sequence variants were consistently found as most abundant in the adults, regardless of the sample collection site, and all belonged to the Gammaproteobacteria . Our data suggests that these bacteria were not randomly derived by chance from the environment in the mosquito but rather deposited by a female mosquito during oviposition, a transmission route recently coined as “diagonal transmission”. Indeed, our results indicated that there is a selection of Gammaproteobacteria from the breeding water and that these bacterial members are further maintained from larvae to adult. This study provided new data on the microbiome composition of field-captured Ae. aegypti , contributing to an enhanced understanding of the origin and colonization route of the mosquito microbiome, potentially via a diagonal transmission route. Importance The past decades the world has experienced a vast increase in epidemics of pathogenic infections transmitted by vectors. These pathogens can cause severe diseases such as haemorrhagic fever, encephalitis, and arthritis. For instance, several arboviruses, such as chikungunya virus, Zika virus, and dengue virus, pose significant global health threats because of their high disease burden, their widespread (re-)emergence and the lack of (good) anti-arboviral strategies. Despite the clear burden, current vector control strategies are clearly insufficient. A promising strategy is the usage of microorganisms to tackle vector-borne transmission. However, a better fundamental understanding of their functioning in the vector is needed. Particularly, how microorganisms in the field develop inside the insect body and are transmitted between different life stages remains intensively debated. We addressed this knowledge gap by studying the mosquito microbiome in African Aedes aegypti mosquitoes at different sampling locations, ranging over different mosquito life stages, and including the environmental water.