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The population structure of sprat (Sprattus sprattus) in the Swedish Kattegat – Skagerrak has been at present not well investigated, and the boundaries between the management unit in this region and the larger stock occurring in the North Sea are also highly uncertain, posing issues to the successful management of the stock in this area. \n \nIn this study, variations in otolith shape among several samples from the Swedish west coast, southern North Sea and Norwegian fjords north of Bergen were studied to investigate the effectiveness of shape analysis for characterise the population structure in the study area, and evaluate whether differences could be used to assign individual fish to their origin. \n \nOtolith sample were partitioned by age, and the shape variations and the relations between shape and size were mapped by means of Wavelet and quantitative shape analysis using digitally acquired otolith profiles. The areas of the otolith showing the highest proportion of variation were identified, and classification techniques were used to investigate the spatial clustering of these variations along the study area. \n \nNo differences in otolith shape were observed between left and right otoliths or between male and female individuals of sprat, suggesting that collections of mixed samples collated opportunistically from available collections can be analysed confidently for instance regardless sex in this species. The shape differences among the different geographic locations were observed to occur mainly between the morphological structures of rostrum and excisura major, and allowed to identify three major clusters. The samples from the Norwegian fjords were the most different in shape among all the groups compared in this study, while the Skagerrak – Kattegat and North Sea samples showed a high degree of similarity. A high differentiation was found for the samples within the Uddevalla fjord system in Sweden, suggesting an isolated unit in this fjord. \n \nA latitudinal gradient of differentiation was also observed in the central – southern Kattegat, but the sample size for this region was limited. \n \nClassification success of the Norwegian samples was rather high, as well as assignment of the southern Kattegat fish in the ages 1 to 3, while values between 31 and 78% were computed for the Uddevalla fjords. The classification success between North Sea and Skagerrak individuals based on otolith shape was particularly low as expected given the low level of differentiation. \n \nOur results are consistent with recent genetic findings and the two methodologies corroborated each other at a recent benchmark of sprat stock assessment. In conclusion, this study shows that otolith shape analysis is a promising tool to identify sprat population structure for management purposes.