Mosquitoes are important vectors of pathogens due to their blood feeding behavior. Aedes aegypti (Diptera: Culicidae) transmits arboviruses, such as dengue, Zika, and Chikungunya. This species carries several bacteria that may be beneficial for its biological and physiological development. Therefore, studying the response of its microbiota to chemical products could result in vector control. Recently, imidazolium salts (IS) were identified as effective Ae. aegypti larvicides. Considering the importance of the mosquito microbiota, this study addressed the influence of IS on the bacteria of Ae. aegypti larvae. After exposition of larvae to different IS concentrations, the cultured microbiota was identified through culturomics and mass spectrometry, and the non-cultivated microbiota was characterized by molecular markers. In addition, the influence of the IS on axenic larvae was studied for comparison. There was an alteration in both cultivable species and in their diversity, including modifications in bacterial communities. The axenic larvae were less susceptible to the IS, which was increased after exposing these larvae to bacteria of laboratory breeding water. This highlights the importance of understanding the role of the larval microbiota of Ae. aegypti in the development of imidazolium salt-based larvicides. Such effect of IS towards microbiota of Ae. aegypti larvae, through their antimicrobial action, increases their larvicidal potential
