The whitefly Bemisia tabaci (Gennadius) is a complex of cryptic species, some of which, namely the Mediterranean (MED) and the Middle East–Asia Minor 1 (MEAM1), are highly invasive and injurious crop pests worldwide and able to displace local genotypes. Invasiveness of B. tabaci may depend on the phenotype of inherited bacterial endosymbionts. Here, the B. tabaci genetic diversity variation that has occurred in recent years in southern Italy was examined. Whitefly was genotyped by restriction fragment length polymorphism analysis of polymerase-chain-reaction-amplified fragments (PCR-RFLP) of the COI gene and molecular identification of endosymbionts. Possible factors leading to the observed genetic diversity were examined.