Genetic sequences (16S rRNA) demonstrated that the symbiotic bacteria associated with different populations of the rice brown planthopper, Nilaparvata lugens Stål, were clustered into 18 operational taxonomic units. Molecular phylogenetic analyses revealed that the majority of these bacteria belong to Alphaproteobacteria (Wolbachia), Gammaproteobacteria (Arsenophonus, Acinetobacter, Serratia, Arthrobacter), and the Bacteroidetes (Chryseobacterium, Sphingobacterium). Bacteria of the genera Acinetobacter, Serratia, and Arthrobacter were present in all brown planthopper individuals analyzed. The infection frequency (IF) of Arsenophonus in brown planthopper reared on the rice variety ‘Taichun Native1′ was higher than that observed with the ‘Mudgo' and ‘ASD7′ varieties. The IF of Arsenophonus increased by 50% when the planthoppers were reared on Taichun Native1 for >15 generations, unrelated to the origin of that population of planthoppers. The IF of Wolbachia, however, declined when the brown planthoppers were maintained on a single rice variety under laboratory conditions for several generations. These results suggest that the symbiotic bacteria varied with brown planthopper populations and might have an effect on the adaptation and evolution of brown planthopper on different rice varieties.