The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is a worldwide pest and a vector of numerous plant viruses. B. tabaci is composed of dozens of morphologically indistinguishable biotypes and its taxonomic status is still controversial. This phloem-feeder harbours the primary symbiont Portiera aleyrodidarum and potentially six secondary symbionts: Cardinium, Arsenophonus, Hamiltonella, Rickettsia, Wolbachia and Fritschea. In the southwest Indian Ocean, La Réunion hosts two biotypes of this species: B (invasive) and Ms (indigenous). A multiplex PCR was developed to study the symbiont community of B. tabaci on La Réunion. Symbiont community prevalence and composition, host mitochondrial and nuclear genetic diversity, as well as host plant and localization, were described on field populations of La Réunion for B and Ms B. tabaci biotypes and their hybrids. A clear association between symbiotypes and biotypes was shown. Cardinium, Arsenophonus and Rickettsia were found in the Ms biotype (73.6%, 64.2% and 3.3%, respectively). Hamiltonella (exclusively) and Rickettsia were found in the B biotype (78% and 91.2%, respectively). Hybrids harboured all symbiotypes found in Ms and B populations, but with a higher prevalence of Ms symbiotypes than expected under random hybridization. An unexpected majority was Cardinium mono-infected (65.6%), and a striking minority (9%) harboured Cardinium/Arsenophonus. In the hybrids only, genetic diversity was linked to symbiotype. Among the hybrids, significant links were found between symbiotypes and: (i) mitochondrial COI sequences, i.e. maternal origin; and (ii) alleles of nuclear microsatellite loci, specific to either Ms or B parental biotype. Taken together, our results suggest that Cardinium and/or Arsenophonus may manipulate the reproduction of indigenous (Ms) with invasive (B) biotypes of Bemisia tabaci.