Abstract:[Objective] To study the species and community structure of bacteria in winged and wingless Megoura crassicauda (Mordvilko). [Methods] Illumina MiSeq high-throughput sequencing was carried out for the V3-V4 variable region of bacterial 16S rRNA gene. [Results] A total of 4 746 449 sequences were obtained and annotated to 586 operational taxonomic units (OTUs) belonging to 477 species, 336 genera, 192 families, 106 orders, 46 classes of 25 phyla. Firmicutes, Actinobacteria, Proteobacteria, and Cyanobacteria were the dominant phyla in all samples. The dominant genera included Staphylococcus, Corynebacterium, and Buchnera. At the phylum level, the relative abundance of Proteobacteria, Cyanobacteria, and Deinococcus-Thermus in the winged morph was significantly higher than that in the wingless morph. At the genus level, the relative abundance of Buchnera, Exiguobacterium, Pseudomonas, Glutamicibacter, and Pseudonocardia in the winged morph was significantly higher than that in the wingless morph. [Conclusion] This study clarified the diversity and community structure of the bacteria in winged and wingless M. crassicauda and provided a reference for exploring the role of bacteria in the wing differentiation of aphids and developing new methods for pest control.