Whiteflies (suborder Sternorrhyncha, family Aleyrodidae) are known to harbor prokaryotic symbionts, some of which are vital and provide specific nutritional needs, while others are transient or nonessential, that can either be beneficial or deleterious in the long-term. However, the extent to which diverse bacterial symbionts are associated with populations of the same species of whitefly that colonize herbaceous plants in diverse habitats, and their particular influence on the evolution of the whitefly host, are not well studied. Here, the composition and diversity of prokaryotic symbionts associated with biotypes or haplotypes of the whitefly Bemisia tabaci Gennadius were examined for collections from representative host plants and different geographical locations worldwide. The eubacterial 16S ribosomal DNA (rDNA) and Wolbachia-specific 16S rDNA genes for endosymbionts were obtained by polymerase chain reaction (PCR) amplification. Amplification and comparison of 16S rDNA sequences revealed that a primary-like symbiont was associated with all whitefly collections examined. However, the endosymbiont 16S rDNA phylogeny was not strictly concordant with the phylogeographically informative cytochrome oxidase I tree for the respective whitefly host. Secondary symbiont sequences for 13 of 20 whitefly populations clustered with Arsenophonus spp. and aphid T-type bacteria, which both belong to the Enterobacteriaceae. PCR and sequencing of Wolbachia-specific 16S rDNA revealed that at least 33% of B. tabaci populations harbored Wolbachia.