Whiteflies comprise a complex of cryptic species that are genetically distinct but morphologically indistinguishable. Among them, Bemisia tabaci and Trialeurodes vaporariorum (Tvap) are the most prominent species causing agricultural damage. In Brazil, three B. tabaci species have been identified: New World (NW), Middle East-Asia Minor (MEAM1), and Mediterranean (MED). Whiteflies establish symbiotic associations with endosymbiotic bacteria, conferring adaptive advantages to the insects. The objective of this study was to identify whitefly species in municipalities of the state of Paraná and investigate their interactions with endosymbiotic bacteria. Insects were collected in 14 municipalities across different edaphoclimatic regions of Paraná, either in agricultural crops or on weeds. Molecular analyses, based on previously published PCR-based methods, were used to identify the insects and their respective endosymbionts. The results revealed that B. tabaci MEAM1, MED, NW, and Tvap accounted for 39.8%, 27.0%, 6.3%, and 23.7% of the collected specimens, respectively. These insects exhibited interactions with endosymbiont genera such as Portiera, Arsenophonus, Rickettsia, Hamiltonella, and Wolbachia, either in isolation or through co-infection. In some instances, interactions with up to five endosymbionts were observed in specific locations. The occurrence of Tvap in open fields and the prevalence of MED, particularly in the southeast of the state, where temperatures are milder, along with their interactions with endosymbionts providing adaptive advantages to the insects, raise significant phytosanitary concerns for the agricultural security of Paraná.