Two Macrolophus species, M. melanotoma (=M. caliginosus) and M. pygmaeus, have been referred to as efficient predators of several key pests on vegetable crops in Europe. However, due to the great morphological similarity of these species, they have been confused, with important consequences for inoculative releases of these predators in greenhouses and for the conservation of their natural populations on greenhouse and outdoor crops. In this work, we developed tools to identify these morphologically very similar species. We first confirmed the specific status of two Macrolophus populations collected on their respective host plants (Dittrichia viscosa and tomato) through crossing experiments. Then, using multivariate morphometric analysis, we proposed a linear discriminant function that combines head measurements separating males from the two species without error. Finally, we designed specific primers for a mitochondrial DNA region that were able to distinguish field-collected Macrolophus individuals through conventional PCR. In conclusion, the tools developed in the present study will allow reliable identification of the Macrolophus species present in crops and in the native flora that are the source of populations that colonise them. They will also allow correct identification of mass reared Macrolophus to be introduced in greenhouse crops in inoculative releases.