Otolith shape variation of seven herring stocks in the Northeast Atlantic and Canada was studied to see if otolith shape can be used to discriminate the stocks. The otolith shape was obtained using quantitative shape analysis, transformed with Wavelet and analysed with multivariate methods. Otolith shape differences were detected among the seven stocks, which could be traced to three morphological structures. These shape differences could classify between Icelandic summer spawners and Norwegian spring spawners with 75% accuracy, but these stocks are known to mix at feeding grounds east of Iceland. This study provides a method which can be used as a discriminating tool for stock identification of herring and the technique can be applied to other fish species as well.