[Objectives]  The infection rates and taxonomic relationships between Wolbachia strains in the sister species Ectropis obliqua and E. grisescens (Lepidoptera: Geometridae) were identified by molecular methods in order to reveal the potential effects of this endosymbiont on these species. [Methods]  Wolbachia infection in three populations of E. obliqua (Hangzhou and Yuhang, Zhejiang province; Wuxi, Jiangsu Province) and three populations of E. grisescens (Xinchang, Zhejiang Province; Xishui, Hubei Province; and Nanchang, Jiangxi Province) were detected using PCR with three specific primers for Wolbachia 16S rRNA and the Wolbachia ftsZ and wsp genes. All Wolbachia 16S rRNA, ftsZ and wsp genes from the three E. grisescens populations and some Wolbachia 16S rRNA and wsp genes from the three E. obliqua populations, were sequenced and analyzed. [Results]  All E. obliqua and E. grisescens populations were infected with Wolbachia. Infection rates of the three E. grisescens populations were all 100%, but ranged from 22% to 95% among the three E. obliqua populations, with positive PCRs showing only weak bands in the electrophoretogram. There were no intra- and interspecific differences in the wsp sequences of E. obliqua and E. grisescens, however, intra- and interspecific differences in 16S rRNA sequences were between 0.362% and 0.727%, respectively. There was a 1.647% difference in two ftsZ haplotypes from E. grisescens, moreover, we were unable to successfully amplify ftsZ from all E. obliqua individuals. A phylogenetic tree based on the 16S rRNA and wsp sequences showed that all strains of Wolbachia detected belong to the Pip subgroup of the B group. [Conclusion]  All three E. obliqua and E. grisescens populations tested are infected with Wolbachia strains belonging to the Pip subgroup of the B group, but the infection rate varies significantly between E. obliqua and E. grisescens. These results provide the basis for future study of the effects of Wolbachia on the biology and ecology of E. obliqua and E. grisescens.