[Objectives]  Insects are often infected by the endosymbiotic bacteria Arsenophonus, Wolbachia, Spiroplasma and Cardinium and the detection and analysis of these bacteria in different geographic populations of the brown planthopper could provide information helpful for the control of this pest. [Methods]  Specimens from 14 geographic brown planthopper populations were collected in 2014 and 2015, and their endosymbiotic bacteria identified with PCR. Phylogenetic trees were constructed using Mega5.01 based on variation in the 23S rRNA gene of Arsenophonus and the 16S rRNA gene of Wolbachia detected in brown planthopper specimens. [Results]  Spiroplasma and Cardinium were not detected in any samples. In 2014, the highest Wolbachia and Arsenophonus infection rates, 20% and 30%, respectively, were detected in the Hechi population. In 2015, the highest Wolbachia and Arsenophonus infection rates, 30% and 20%, respectively, were detected in the Nanjing and Changsha populations. Phylogenetic analysis revealed that Arsenophonus detected in the brown planthopper populations sampled was most closely related that found in the Homoptera. With the exception of the Haikou population, which was infected with the Wolbachia A supergroup, all other brown planthopper populations were infected with the Wolbachia B supergroup. There was no evidence of co-infection by Arsenophonus and Wolbachia. [Conclusion]  The infection rates of Arsenophonus and Wolbachia varied among different geographical populations of the brown planthopper. More females were infected with Wolbachia than males. The Arsenophonus 23S rRNA gene and the Wolbachia 16S rRNA genes found in brown planthoppers are similar to those in other insects. There was no evidence of co-infection of by Arsenophonus and Wolbachia in the brown planthopper populations sampled, nor were Spiroplasma and Cardinium detected in any of the sampled populations.