In the Baltic Sea, several stocks of herring (Clupea harengus L.) are surveyed and managed separately. For assessment purposes, a spatial stock separation based on ICES subdivisions is implemented. However, especially in the western Baltic, the distribution areas of two stocks, the western Baltic spring-spawning herring and the central Baltic herring, overlap. Results of regularly conducted surveys for assessment purposes indicated variable degrees of mixing of both stocks in the survey area, based on conspicuous differences in weights/lengths within certain age groups, especially in an area known for overlapping distribution of both stocks. At present, varying fractions of the central Baltic herring stock have not been taken into account during regular surveys conducted in the western Baltic, leading to possible undetected biases in assessment indices derived from these surveys. Additionally, methods otherwise applied for stock separation of Baltic herring so far are based on parameters that cannot readily be derived during regular surveys. In this paper, we present a simple and quick method to reliably allocate herring to either stock based on a separation function derived from survey-based length-at-age data, thus facilitating a more precise estimate of biomass and abundance indices from regular surveys and commercial fisheries.