The applicability of the otolith shape analysis of the European sardine, Sardina pilchardus was investigated to help in stock discrimination. Discriminant analysis was achieved by an otolith-based morphometrics assignment of otolith shape; 360 specimens of S. pilchardus were collected from three localities (Larache, Safi and Dakhla). Otolith shapes were described from otolith measurements and elliptic Fourier descriptors. This analysis showed the presence of three different morphotypes in the studied locations. The existence of three morphotypes is probably related to the variation of oceanographic conditions impacting the feeding regime and fish growth. This study proved that otolith shape analysis could become an accurate marker for S. pilchardus population discrimination.