The assignment of individual fish to its stock of origin is important for reliable stock assessment and fisheries management. Otolith shape is commonly used as the marker of distinct stocks in discrimination studies. Our literature review showed that the application and comparison of alternative statistical classifiers to discriminate fish stocks based on otolith shape is limited. Therefore, we compared the performance of two traditional and four machine learning classifiers based on Fourier analysis of otolith shape using selected stocks of Atlantic cod (Gadus morhua) in the southern Baltic and Atlantic herring (Clupea harengus) in the western Norwegian Sea, Skagerrak and the southern Baltic Sea. Our results showed that the stocks can be successfully discriminated based on their otolith shapes. We observed significant differences in the accuracy obtained by the tested classifiers. For both species, support vector machines (SVM) resulted in the highest classification accuracy. These findings suggest that modern machine learning algorithms, like SVM, can help to improve the accuracy of fish stock discrimination systems based on the otolith shape