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Parasitoid wasps from the Aphelinidae family (Hymenoptera) are important control agents of Bemisia tabaci(Gennadius, 1889) cryptic species,both through reproduction and feeding processes. Identifying native parasitoid species within agricultural systems affected by Bemisiawhitefly species is the first step to developing guidelines for the creation and release of biological control agents aiming at this highly damaging pest species complex. Taxonomic and phylogenetic analyses based on morphological and molecular characters, respectively, confirmed the occurrence of Encarsia formosa(Gahan, 1924) in greenhouse tomatoes from Santa Maria, Encarsia porteri(Mercet, 1928) in open-field soybean from Santa Maria, and Eretmocerus mundusMercet, 1931 in greenhouse tomatoes from São José do Hortêncio, all within Rio Grande do Sul state (South Brazil). This is the first report of En. formosa, En. porteriand Er. mundusparasitising B. tabaciin South Brazil, and the first En. porteripartial mtCOI gene sequence being reported and characterised. The high temperature inside the tomato greenhouses can be a possible cause for the predominance of Er. mundusin São José do Hortêncio, and sex ratios in the surveyed populations point to female and male prevalence within Encarsiaand Eretmocerusgenera, respectively. The combined use of taxonomic and molecular characterisation highlights the importance of combining both morphological and molecular approaches in the assessment of previously unidentified whitefly parasitoids.