In this study, the relationships among and the taxonomic status of three closely related parasitic wasps that are widely used as biological control agents of cereal aphids, Aphidius uzbekistanicus Luzhetzki, Aphidius rhopalosiphi De Stefani Perez, and Aphidius avenaphis (Fitch), were examined. Genetic divergence at an average of 6% was recorded between A. uzbekistanicus and A. rhopalosiphi by using the mitochondrial (mt) gene cytochrome oxidase I (COI) barcoding region. Identical mtCOI gene sequences were observed in A. uzbekistanicus specimens that originated from Eurasia and in the North American species A. avenaphis. The haplotype fluctuation in A. rhopalosiphi specimens that originated from the west Palaearctic was an average of 1.5% (maximum, 2.4%). In contrast, specimens of A. uzbekistanicus from central and western parts of Eurasia were largely homogenous, with only a single mutation recorded in a specimen from eastern Europe (Serbia). The morphological and genetic diversity found in A. rhopalosiphi may suggest the existence of cryptic species, especially for lineages that have a large degree of mtCOI diversity and sympatric occurrence. The geometric morphometric analysis of stigma shape presented in this study demonstrated that members of A. uzbekistanicus have a shorter forewing r vein and a more elongated stigma, relative to those of A. avenaphis. Our research validates the use of stigma shape and flagellomere 1 color for morphological discrimination between wasp species.