Abstract Fish stocking is one of the most widespread and frequent management strategies in freshwater systems. However, the contribution of stocked fish to the population is seldom investigated, and hence the effectiveness of this strategy is virtually unknown for many populations. Understanding the contribution of stocked fish into the population is crucial because it allows the disentanglement of the confounding effects generated by allochthonous individuals into the estimation of survival and growth rates of the population. To discriminate between the allochthonous and autochthonous individuals in a population, the shape of sagittae otoliths from pikeperch (Sander lucioperca) where compared. Results indicated significant differences among stocked and non-stocked fish, with the former having smaller and wider sagittae otoliths than the latter. Our results suggest that this technique can be used to discriminate the natal origin of fish in a much faster and cheaper way than commonly used techniques.