Abstract The Barcode Index Numbers (BINs) are operational species units based on patterns of COI divergences that in most cases correspond to species. It has been repeatedly observed that more than one BIN can be found under the same species name particularly when large geographic scales are considered. One such case concerns Eupithecia conterminata, a species widespread in North European countries and restricted to mountainous regions in the rest of the continent, for which five BINs are found in Europe. In order to solve the question concerning the taxonomic status of these BINs and European populations, we employed an integrated approach by combining classical morphological traits (genitalia and wing markings) with those of molecular data, the latter involving both mitochondrial and nuclear genes. This approach allowed us to recognize two valid species in Europe, E. conterminata, currently known only in Fennoscandia, Baltic countries and Russia, and Eupithecia manniaria sp. rev., with distribution covering Central and South European countries. We furthermore synonymized Eupithecia pindosata syn. nov. from Greece with E. manniaria. The European range of these species and their mitochondrial diversity appear to be coherent with biogeographical histories of their foodplants Picea abies and Abies species.