The whitefly Bemisia tabaci is a complex of morphologically indistinguishable species and is one of the most destructive insect pests worldwide. This pest is multivoltine, highly polyphagous and a vector to important plant viruses including the cassava brown streak virus and the cassava mosaic virus. B. tabaci cryptic species are known to harbor various bacterial endosymbionts, some of which are know to confer fitness to the host. Here, we conducted genome-wide single nucleotide polymorphism (SNP) analysis using a Nextera-tagmented, reductively amplified DNA protocol (nextRAD) to investigate the phylogenomics of the Bemisia cryptic invasive species complex and study their endosymbiont metacommunities. We ascertained levels of endobacterial abundances in cryptic host species, identified reads mapping to primary (i.e. Candidatus Portiera aleyrodidarum) and secondary endosymbionts (e.g., C. Hamiltonella defensa), and explored patterns of host-endosymbiont co-evolutionary relationships from these diverse classes of primary- and secondary-endosymbionts through the endosymbionts’ genome-wide SNP data. Our findings will have implications for further understanding the effect of bacterial endosymbionts on the host evolutionary ecology.