Wolbachia are a common and widespread group of symbiotic bacteria found in the reproductive tissues of arthropods. Bactrocera dorsalis (Hendel) is an important pest causing considerable economic losses of fruits and vegetables in several southern provinces of China. In this study, polymerase chain reaction (PCR) with general Wolbachia surface protein (wsp) primers was used to test the presence of Wolbachia in 1,500 individuals of B. dorsalis from five geographical populations of China. We detected 19 individuals of B. dorsalis infected by Wolbachia, and the infection rates of different populations varied. Comparison of wsp gene sequences from 19 individuals and search of the GenBank identified four new sequences, probably representing four Wolbachia strains. Sequence comparison showed that the four Wolbachia strains from B. dorsalis in China belonged to three groups (Kue, Mel, and Cuc). Phylogenetic analysis of the wsp sequences suggests that geographical isolation of Wolbachia exists among the populations of B. dorsalis in China, and gene flow of Wolbachia might have occurred between B. dorsalis populations of China and Thailand. Phylogenetic analysis performed on the host mitochondrial cytochrome oxidase I (COI) gene and wsp gene suggests that host has coevolved with Wolbachia.