Wolbachia, a bacterial symbiont, is maternally transmitted in arthropods and nematodes. We report a systematic survey of Wolbachia taxonomy in the sweetpotato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), and in some of its natural enemies. For the first time, Wolbachia infections in B. tabaci are correlated with various whitefly genetic groups, host plants, and natural enemies as well as with geographical regions. Polymerase chain reaction using 16S rDNA and ftsZ genes revealed two Wolbachia supergroups, A and B, exist as single or double infections in B. tabaci as well as in some of its aphelinid parasitoids and predatory beetles. Approximately 89% of B. tabaci sampled were infected by Wolbachia, among which 34% were infected by A, 51% were infected by B, and 5% were infected by both A and B supergroups. These infection frequencies differed among B. tabaci genetic groups and locations. The invasive B. tabaci genetic group from the Middle East Asia Minor 1 (also referred as B biotype) and Mediterranean (also referred as Q biotype) was more likely to harbor A than B, whereas native genetic groups in AsiaI and AsiaII were more likely to harbor B than A. Although 60% of aphelinid parasitoids and 72% of coccinellid beetles also were infected by Wolbachia, they were more likely to host B than A. Furthermore, for the first time we report Wolbachia in B biotype from specimens collected outside of China. Construction of a phylogenetic tree clearly indicated that the Wolbachia sequences from different genetic groups of B. tabaci were not only similar to each other but also to sequences from beetles and parasitoids, which may provide evidence of coevolution and horizontal transmission of Wolbachia populations.