Endosymbionts are widely distributed among insects via intraspecific vertical transmission and interspecific horizontal transmission. Parasitoids have attracted considerable interest due to their possible role in the horizontal transmission of endosymbionts. Horizontal transmission of endosymbionts between whiteflies via parasitoids has been revealed in the laboratory. However, whether this occurs under field conditions remains unknown. Here, the diversity and phylogenetic relationships of endosymbionts in 1,350 whiteflies and 36 parasitoids that emerged from whitefly nymphs collected from three locations in Jiangsu Province of China were investigated. Only Rickettsia and Wolbachia were identified in both whiteflies and parasitoids, with an overall infection frequency of 22.67% in whiteflies and 16.67% in parasitoids for Wolbachia and of 12.15% in whiteflies and 25% in parasitoids for Rickettsia. Despite the distant relationship between whiteflies and their parasitoids, phylogenetic analyses revealed that the Rickettsia and Wolbachia individuals collected from the two types of organisms were grouped together. Furthermore, shared haplotypes were also identified, which was consistent with the horizontal transmission of endosymbionts between parasitoids and whiteflies. In addition, a parasitoid resistance-related symbiont, Hamiltonella, was detected in whiteflies at a 100% infection frequency, probably accounting for the relatively low parasitism of the whiteflies in the field. The factors affecting the infection frequency of the four secondary endosymbionts in whiteflies were also examined.