Landmark‐based geometric morphometric analysis revealed differences in scale shape between European sardine Sardina pilchardus and round sardinella Sardinella aurita as well as among the local populations of each species. Fish scale measurements from four different areas in the central and eastern Mediterranean Sea showed that the mean scale shape of the two species using landmark data could be differentiated with high certainty. Populations of S. aurita from the central and eastern Mediterranean Sea could be separated reliably (P < 0·001) with an average discrimination rate of 91%, whereas the average discrimination of the S. pilchardus populations was lower (80%), albeit still high.