Brachycaudus helichrysi is a worldwide polyphagous aphid pest that seriously damages its primary hosts (Prunus spp.) and the various cultivated plants among its secondary hosts (e. g. sunflower). A recent study of the Brachycaudus genus suggested that this species might encompass two differentiated lineages. We tested this hypothesis, by carrying out a phylogenetic study of this aphid pest based on worldwide sampling and the evaluation of mitochondrial, nuclear and Buchnera aphidicola DNA markers. We show that this species is actually an amalgamation of two sibling taxa, B. helichrysi H1 and B. helichrysi H2, that seem to have overlapping geographic ranges and herbaceous host plant preferences. These two taxa displayed levels of genetic divergence as great as those generally found between sister species in the Brachycaudus genus, suggesting that they actually correspond to two distinct species. Our phylogenetic reconstructions revealed a degree of incongruence between the topologies obtained with the aphid gene data set and with data for a DNA marker from its primary endosymbiont. We identified possible reasons for this observation and discuss the ecological and genotypic data suggesting that B. helichrysi H1 and B. helichrysi H2 have different life cycles.