AbstractEncarsia pergandiella Howard, described from North America (USA), and Encarsia tabacivora Viggiani, described from South America (Brazil) (Hymenoptera: Aphelinidae), are two formally recognized taxonomic entities, that have been treated by several authors as synonyms due to lack of strong diagnostic characters. Taxonomy of these species is further complicated because several populations, geographically separated and differing in their biology, have been included under the concept of E. pergandiella. Among these, a population originally collected in Brazil and introduced to North America reproduces by thelytokous parthenogenesis and is infected by the symbiont Cardinium, while a morphologically indistinguishable population, naturally occurring in Texas, is biparental and infected by a related strain of Cardinium that induces cytoplasmic incompatibility. A third population known from California and introduced to the Old World is biparental and uninfected by intracellular symbionts. While adult females of the first two populations have entirely light yellow bodies and pupate face up (light form), those of the third population have largely brown bodies and pupate face down (dark form). Other dark form populations are known from Texas, Florida and New York. Because these parasitoids are economically important biological control agents of cosmopolitan whitefly pests, it is critical to characterize them correctly. In this study, we integrated molecular and morphometric analyses to substantiate observed differences in biological traits, and resolve the complicated taxonomy of this species complex. We sequenced the mitochondrial cytochrome c oxidase subunit I gene and the D2 region of the ribosomal 28S gene for individuals of both light form (from Texas and Brazil) and dark form (from California, Texas, Italy and Canary Islands) originating from laboratory cultures or collected in the field. Phylogenetic analysis unambiguously distinguished three well‐supported groups corresponding to the Texas light form, the Brazil light form and the dark form. Individuals of these three groups, in combination with all available type material (E. pergandiella, its synonym Encarsia versicolor Girault and E. tabacivora) and additional museum specimens of the dark form from New York and Italy, were subjected to multivariate morphometric analyses using Burnaby principal component analysis followed by a linear discriminant analysis, and multivariate ratio analysis. Overall, the analyses showed that: (i) E. pergandiella and E. tabacivora are two distinct species; (ii) the thelytokous Brazil light form corresponds to E. tabacivora; (iii) the biparental Texas light form is a new species formally described here as Encarsia suzannae sp.n.; (iv) two new biparental species can be referred to the dark form, one described as Encarsia gennaroi sp.n. including the populations sampled in California, Texas, Italy and Canary Islands, and the other corresponding to the population from New York described as Encarsia marthae sp.n. A dichotomous key for both sexes of the species of the E. pergandiella complex is provided for identification.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:278475A0‐C2C4‐4400‐A042‐A5716457829D.