The Moroccan Atlantic coast (21–36°N) is part of one of the most productive marine eastern boundary upwelling ecosystems worldwide. Nevertheless, information about the structure of its exploited fish populations is scarce. In this study, whole otolith elemental signatures of 111 hake (Merluccius merluccius) and 118 of sardine (Sardina pilchardus), sampled during the period June 2012 - July 2013 in 11 locations along the Moroccan coast, were analysed by solution based ICP MS. These 2 species were selected for their importance in the fisheries, their contrasted life histories, and differences in trophic behavior. Whole otolith comparisons used Ba/Ca, Li/Ca, Mg/Ca, Mn/Ca, Rb/Ca, Sc/Ca, Sr/Ca, to demonstrate the regional population structures. The linear discriminant analysis of whole otolith chemistry data of hake and sardine reached respectively 88 % and 71 % mean adequate classification, and rose to 100 % within the identified groups. The spatial variation in the elemental composition of the otoliths of the two species were significant, and all showed a clear geographic cut, thus identifying a northern and a southern group. The major split for the two species occurred in the same area corresponding to the transition zone between the northern temperate mud-shelf ecosystem and the arid ecosystem at the south (28–29°N). Complex oceanographic processes may act in this area as a barrier to planktonic dispersion favouring isolation processes that lead to distinct populations. These findings are new to hake and confirm previous studies on sardine population structure, and should be considered in fisheries management to better match management units and stock structure.