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Bemisia tabaci (Aleyrodidae family) is an insect vector of plant viruses that affects a wide variety of crops around the world. In the following study, we analyzed the variation in the bacterial communities associated with natural populations of B. tabaci (MEAM1) of four different crops from six regions from Mexico semi-arid zone (Baja California Sur). PCR was used to amplify the mitochondrial cytochrome oxidase I gene (mtCOI), and then to carry out the phylogenetic analysis for genetic identification of the isolated B. tabaci. Next generation sequencing coupled with 16S metagenomic analysis was applied in order to characterize B. tabaci inner microbial community. Finally, bacterial obligate symbiont and facultative symbiont were confirmed by PCR amplification and by phylogenetic analysis. Ours results pointed toward that B. tabaci MEAM1 inner bacterial communities were predominantly structured by Proteobacteria phylum. Moreover, the most represented endosymbionts were the obligate endosymbiont from the genus “Candidatus Portiera”, as well as two facultative symbionts belonging to genera Rickettsia and Hamiltonella; both obligate and facultative endosymbionts were present for all samples, and their relative abundance varied was crop-independent. Geographic localization and insect diet play a central role to maintain bacterial community structure of the B. tabaci MEAM1 whitefly at phylum taxonomic level. Agricultural practices were a factor that affected samples of bacterial community structure similarities, reflected in samples clustering. Host plants that are part of B. tabaci diet did not influence directly, in spite of sap nutrient differences, into obligate and facultative endosymbionts relative abundance.