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The otolith, found in both inner ears of bony fish, has mainly been used to estimate fish age. Another application that has been developing significantly in recent years, however, is the use of otolith shape as a tool for stock identification. Often, studies have directly used the shape asymmetry between the right and left otoliths. We tested the magnitude of directional asymmetry between the sagittal otoliths (left vs. right) of 2991 individuals according to their catch locations, and we selected species to evaluate whether directional asymmetry may itself be a tool to evaluate stock boundaries. Elliptical Fourier descriptors were used to describe the otolith shape. We used a flatfish, the common sole (Solea solea, n = 2431), from the eastern English Channel and the southern North Sea as well as a roundfish, the bogue (Boops boops, n = 560), from the Mediterranean Sea. Both species showed significant levels of directional asymmetry between the testing locations. The bogue otoliths showed significant asymmetry for only 5 out of 11 locations, with substantial separation between two large areas: the Algerian coast and the western part of the Italian coast. The sole otoliths showed significant asymmetry in the shape analysis (3.84–6.57%), suggesting a substantial separation between two large areas: the English and French parts of the English Channel and the southern North Sea. Consequently, directional bilateral asymmetry in otolith shape is a potential new method for stock identification.