Stock identification studies are essential to understanding fish population structure and connectivity across wide geographical areas, and thus contribute to efficient fisheries management. The blackbelly rosefish, Helicolenus dactylopterus, and European hake, Merluccius, are two economically important marine fishes, but there are still gaps in knowledge regarding their present stock structure. Our objective was to assess the ability of otolith shape to define stock structure for the two species along the Northeastern Atlantic Ocean and the Mediterranean Sea, based on samples from eight and seven areas, for blackbelly rosefish and European hake, respectively. Shape analysis was obtained through Wavelet analysis. Canonical analysis of principal coordinates provided significant evidence for different population units with a clear separation between the Atlantic and Mediterranean populations for both species. However, random forest procedures indicated that the discrimination power varied with species and locations. For blackbelly rosefish, various Atlantic populations were more evident than for European hake. Overall, the usefulness of otolith shape to delineate stock structure of two species with distinct life history traits across a broad spatial region from the mid-Atlantic isles to the polar region, as well as the Mediterranean was demonstrated. Moving forward, it will be key to align our growing understanding of population structure with our increasing knowledge on species’ biological traits to ensure management units reflect population structure.