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While otolith shape analysis can provide a valuable tool for discriminating between fish populations, factors which may influence otolith shape, such as the effect of size, directional asymmetry in growth, and local environmental conditions, are often unknown. Here, we analyzed differences in otolith shape across three size classes of age-0 common sole Solea solea L. from nursery grounds off the Belgian coast and in the Wadden Sea. Across size classes, form-factor decreased and roundness remained consistently high in both nursery grounds, while ellipticity increased in the Belgian nursery. Directional asymmetry between left and right otoliths measured by Fourier coefficients accounted for 0.96 and 7.2% of the variance when comparing otoliths overall, and for each size class, respectively. Within the Belgian nursery, results were consistent across sampling years and locations. In addition, otolith shape was marginally different between nursery grounds, but highly variable within nursery grounds. A small divergent group, which seems partly related to fish size, was noted at both spatial and temporal scales. Based on these results and before embarking on a study of population structure using otolith shape in age-0 common sole, we recommend testing for directional asymmetry and fish size effects across the entire region of interest.