Imidacloprid, a neonicotinoid insecticide, is efficacious against hemipterans, including the brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). However, frequent use of this insecticide has resulted in the development of high levels of resistance among brown planthopper populations. Endosymbionts of insects have contributed to host physiology and evolution and play a role in resistance to chemical toxins. In this study, polymerase chain reaction–denaturing gradient gel electrophoresis was used to analyze the bacterial and yeast-like symbiont communities of imidacloprid-resistant and -susceptible brown planthopper populations. The Shannon-Weaver diversity index and the evenness index indicated no differences in the richness and the expression of overall species distribution of the symbiotic communities of resistant and susceptible populations. The similarity coefficients of 0.53 and 0.56 for bacterial and yeast-like symbionts, respectively, indicated the main types of differences among microorganisms in resistant and susceptible populations. Sequence comparison analysis indicated the bacterial species in the susceptible population were members of the Enterobacteriaceae and Moraxellaceae, and those in the resistant population were members of the Enterobacteriaceae, Oxalobacteriaceae, Rhodobacteriaceae, and Sphingomonadaceae. Differences also were found in the composition of yeast-like symbionts of the two populations; Cryptococcus luteolus, Pseudozyma aphidis, and Pseudozyma antarctica were detected in the susceptible population, and Cladosporium perangustum was detected in the resistant population.