ResultsOverall, Proteobacteria and Firmicutes were the dominant bacteria phyla with fluctuating relative abundances across the life stage. Cosenzaea myxofaciens is dominant in adulthood, while Enterococcus silesiacus and Morganella morganii dominate in larvae and pupae of E. balteatus, respectively. Unexpectedly, Serratia symbiotica, one facultative endosymbiont commonly harbored in aphids, was one of the predominant bacteria in larvae of E. balteatus, just behind Enterococcus silesiacus. In addition, S. symbiotica was also surprisingly most dominated in M. crassicauda aphids (92.1% relative abundance), which are significantly higher than Buchnera aphidicola (4.7% relative abundance), the primary obligate symbiont of most aphid species. Approximately 25% mortality was observed among newly emerged adults, of which microbiota was also disordered, similar to normally dying individuals. Sexually biased symbionts and 41 bacteria species with pairwise co-occurrence in E. balteatus and 23 biomarker species for each group were identified eventually. Functional prediction showed symbionts of hoverflies and aphids, both mainly focusing on metabolic pathways. In brief, we comprehensively explored the microbiome in one Syrphidae hoverfly using E. balteatus reared indoors on M. morganii as the model, revealed its dominated symbiont species, identified sexually biased symbionts, and found an aphid facultative endosymbiont inhabited in the hoverfly. We also found that the dominated symbiotic bacteria in M. crassicauda are S. symbiotica other than Buchnera aphidicola.