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 IUCN assessment performed on Moroccan Unio species, recognized the existence of a distinct species, U. foucauldianus, with a Critically Endangered conservation status. The present study delivered new genetic, morphological and geographical distribution data on two Unio sp. (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 10 newly developed microsatellite loci as well as shell morphometry. We suggest that the IUCN critically endangered conservation status of the U. foucauldianus should be revised and probably down-listed since its actual distribution range is much wider than previously described. Phylogenetic relationships with the other Unio sp. 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.