Whiteflies harbor several secondary endosymbionts, which are maternally inherited from mother to offspring, that have major effects on host preferences, biology, and evolution. Here, we identified Wolbachia bacteria in sweetpotato whitefly (Bemisia tabaci) as well as whitefly popluations from other countries by comparison of 16S rDNA sequences. Wolbachia were detected in all tested indigenous B. tabaci populations (Bangladesh, Myanmar, Nepal, and the Philippines) as well as Q1 biotype of Korea, whereas they were absent from B biotype of Korea and Q biotype of China. Wolbachia were also detected in all five tested Aleurodicus dispersus populations as well as Tetraleurodes acaciae, whereas they were not detected in all seven Trialeurodes vaporariorum populatuions. In addiiton, Wolbachia were detected in parasitic wasp (Encarsia formosa) of B. tabaci as well as honeybee (Apis mellifera). Among the 19 whitefly populations from different countries, our analysis identified four phylogenetic groups of Wolbachia, thereby demonstrating the high diversity of this genus. Wolbachia phylogeny suggests a correlation of geographical range with ecological variation at the species level.