Wolbachia is a genus of maternally inherited, intracellular, alpha-Proteobacteria which are widespread among arthropods and cause various reproductive alterations such as cytoplasmic incompatibility and feminization. Wolbachia strains in arthropods have been phylogenetically divided into two supergroups, A and B. Here, we determined the phylogenetic relationships among Wolbachia strains harbored by insects and isopod crustaceans by using groE operon sequences, which encode highly conserved bacterial heat shock proteins. This study includes the first survey for Wolbachia in isopods from a Southeast Asian country, i.e., Thailand. Two isopod species from different parts of Thailand were found to be infected by Wolbachia. Their groE sequences were also included in the phylogenetic analysis. Our results showed clearly that 19 strains from tropical insects, 11 strains from French isopods, and two strains from Thai isopods were in the B supergroup, and 15 strains from tropical insects were in the A supergroup. This is the first report of phylogenetic analysis of a large data set comprising Wolbachia groE sequences from both insects and isopod crustaceans.