Many doubts still exist about which freshwater mussel Unio species inhabit Northwest Africa. While some authors refer to the presence of Unio delphinus in the Atlantic North African basins of Morocco, a recent International Union for Conservation of Nature (IUCN) assessment performed on Moroccan Unio species, recognised the existence of a distinct species, Unio foucauldianus, with a critically endangered conservation status. The present study delivered new genetic, morphological, and geographical distribution data on two Unio species (i.e. U. delphinus and U. foucauldianus) greatly increasing the almost non-existent data on these taxa. Bayesian phylogenetic analysis revealed two highly supported geographically concordant clades, which diverged by 3.2 ± 0.6 % (uncorrected p distance): the first distributed across Iberia and corresponding to U. delphinus, and the second distributed across Morocco, corresponding to U. foucauldianus. These results were corroborated by the analysis of ten newly developed microsatellite loci as well as shell morphometry. We suggest that the IUCN critically endangered conservation status of U. foucauldianus should be revised and probably down-listed since its actual distribution is much wider than previously described. Phylogenetic relationships with the other Unio species were resolved, showing that U. delphinus and U. foucauldianus fall inside the pictorum lineage. The estimated molecular rate reported herein (0.265 ± 0.06 % per million years) represents the first for the Unionida and could be used as a reference in future studies.