In the Western Baltic Sea two genetically distinct cod stocks “Eastern Baltic cod” and “Western Balticcod” occur with considerable mixing of stocks. In this study we evaluated the applicability of otolithshape analysis for classification of individuals caught in the mixed stock cod fishery, using SNP (singlenucleotide polymorphism) based genetic assignment of otolith shape baselines. We further developeda management aimed approach for mixed stock assignment by robust stochastic baseline selection andposterior bias correction by individual reassignment of the least likely classifications into the alternatestock. Classification criteria selected by Monte Carlo runs of Linear Discriminant Analysis were capturedby otolith area and 20 Elliptic Fourier Descriptors of primarily low frequency harmonics. Classificationsuccess was considerably lower when using a baseline of spawning individuals only, compared to thebetter spatial coverage of a combined baseline also including genotyped individuals from the mixed stockarea. Furthermore, the inclusion of genotyped individuals balanced the baseline size composition and toa large extent removed a strong size related bias in classification success. These results demonstrate theinterplay of environmental, ontogenetic and genetic influences on otolith shape, which complicates theapplication of otolith shape for stock discrimination in mixed-stock scenarios. Rigours genetic validationand further studies on the temporal dynamics of shape formation are necessary.