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Gårdmark, A., Östman, Ö., Nielsen, A., Lundström K., Karlsson O., Pönni, J., and Aho, T. 2012. Does predation by grey seals (Halichoerus grypus) affect Bothnian Sea herring stock estimates? – ICES Journal of Marine Science, 69: . Mortality of small pelagic fish due to marine mammals is generally considered to be low compared with other sources of mortality. With recent recoveries of marine mammal predators worldwide, this may no longer hold. The grey seal (Halichoerus grypus) population in the Bothnian Sea has increased fivefold since 1985. Its main prey, herring (Clupea harrengus), is a key species for fisheries in the region. Yet, current stock assessments assume constant natural mortality, leading to a risk of biased stock estimates with increasing predation and misleading analyses of herring population dynamics. We estimated grey seal predation from diet data and reanalysed herring spawning stock biomass (SSB) during 1973–2009. Accounting for predation increased the herring SSB 16% (maximum 19%), but this was within the confidence intervals when ignoring predation. Although mortality in older individuals was inflated when accounting for seal predation, this did not change the conclusions about drivers of herring dynamics. Accounting for grey seal predation is important for abundance estimates of old herring, but currently not for SSB estimates, given the great uncertainties in the standard assessment. The grey seal impact on Bothnian Sea herring will need to be reassessed if stock age composition, grey seal feeding preferences, or total stock development change.