Wolbachia are bacteria that live intracellularly in a wide variety of arthropods. They are maternally inherited and can affect both reproduction and fitness of its host. When infected males mate with uninfected females or females infected by a different Wolbachia strain, there is often a failure of karyogamy, which is usually attributed to cytoplasmic incompatibility (CI). We measured the strength of CI induced by Wolbachia and the fitness effects in three Chinese populations of the brown planthopper Nilaparvata lugens from Hainan, Yunnan, and Guangxi provinces, respectively. No evidence for CI was found in any of the populations, whereas an enhanced fecundity and shortened longevity were observed only in the Hainan population. The infection density was significantly higher in the Hainan population than in the Guangxi population. The Wolbachia strain infecting the three populations appeared to be the same based on the nucleotide sequence of the wsp gene. Therefore, the variable effects of Wolbachia on host fitness seem to be the result of differences in the host genetic background and Wolbachia infection density. The ability of the non-CI-inducing Wolbachia to maintain themselves in their hosts may be attributed to their positive effects on host fecundity and efficient maternal transmission.