Mosquitoes are intensely studied as vectors of disease-causing pathogens, but we know relatively less about microbes that naturally reside in mosquitoes. Profiling resident bacteria in mosquitoes can help identify bacterial groups that can be exploited as a strategy of controlling mosquito populations. High-throughput 16S rRNA gene sequencing and traditional culture-based methods were used to identify bacterial assemblages in Culex quinquefasciatus Say (Diptera: Culicidae) in a tissue- and stage-specific design. In parallel, wild host Cx. quinquefasciatus was compared with our domestic strain. 16S rRNA genes survey finds that Cx. quinquefasciatus has taxonomically restricted bacterial communities, with 90% of its bacterial microbiota composed of eight distinctive bacterial groups: Nocardioidaceae (Actinomycetales), Microbacteriaceae (Actinomycetales), Flavobacteriaceae, Rhizobiales, Acetobacteraceae, Rickettsiaceae, Comamondaceae (Burkholderiales), and Enterobacteriaceae. Taking into account both metagenome- and culture-based methods, we suggest three bacterial groups, Acetobacteraceae, Flavobacteriaceae, and Enterobacteriaceae, as candidates for mutualists in Cx. quinquefasciatus. Members of these three bacterial families have been studied as mutualists, or even as symbionts, in other insect groups, so it is quite possible they play similar roles in mosquitoes.