Whiteflies (suborder, Sternorrhyncha; family, Aleyrodidae) harbor prokaryotic symbionts, some of which are vital and provide specific nutritional needs, while others are transient or nonessential, and can either contribute beneficially or deleteriously. Neither the diversity nor the specific biotic roles of bacterial symbionts associated with the same species of whitefly from diverse habitats are understood. We examined the diversity and some biological contributions for prokaryotic symbionts associated with the Bemisia tabaci complex from different host plants and geographic locations, worldwide. The eubacterial 16S ribosomal DNA and Wolbachia-specific sequences were obtained by polymerase chain reaction. Phylogenetic analyses revealed that a primary symbiont was associated with all collections examined, however, the endosymbiont phylogeny was not strictly concordant with that for the whitefly based on the cytochrome oxidase I gene. Thirteen of twenty haplotypes harbored a secondary symbiont, which clustered in one of two clades in the Enterobacteriaceae. Wolbachia was detected in at least 35% of B. tabaci haplotypes examined, and a Clavibacter-like organism and Clamydia spp. also were associated with certain haplotypes. Certain endosymbionts were found to be directly associated with reproductive isolation in studies involving three distinct haplotypes of B. tabaci.