Wing polyphenism (alate and apterous morphs) in aphids is a trade-off between dispersal and reproduction. How bacterial communities are associated with wing polyphenism in aphids is still not clearly understood. This study used 16S rRNA sequencing to examine the differences in diversity of the bacterial community between alate and apterous morphs in Aphis citricidus, the main vector of the Citrus tristeza virus. Eighty-one operational taxonomic units (OTUs) belonging to 37 orders, 34 classes, and 13 phyla were identified from all samples. Among these OTUs, Wolbachia (79.17%), Buchnera (17.64%), and Pseudomonas (2.99%) were the dominant bacterial genera. The diversity of symbionts varied between the two morphs; apterous morphs had more bacterial diversity (69 OTUs belonging to 45 families, 21 classes, and 12 phyla) than alate morphs (45 OTUs belonging to 36 families, 15 classes, and 10 phyla). In addition, the abundance of five OTUs was significantly different between two morphs. Among these OTUs, two Pseudomonas species (Pseudomonas_brenneri [OTU21] and unclassified_ Pseudomonas [OTU13]) represented a high proportion (3.93% and 2.06%) in alate morphs but were present in low abundance (0.006% and 0.002%) in apterous morphs. RT-qPCR showed consistent results with high-throughput DNA sequencing. The preliminary survey showed the difference in composition and frequency of bacteria between alate and apterous morphs. Thus, the results contribute to anew insight of microorganisms that may be involved in wing dimorphism and helpful for controlling the dispersal of this pest through artificial elimination or reinfection of bacterial symbionts or targeting symbiosis-related host genes by RNA interference in future.