Conservation efforts are often constrained by uncertainty over the factors driving declines in marine mammal populations. In Scotland, there is concern over the potential impact of unrecorded shooting of seals, particularly where this occurs near Special Areas of Conservation. Here, we show that the abundance of harbour seals Phoca vitulina in the Moray Firth, north-east Scotland, declined by 2–5% per annum between 1993 and 2004. Records from local salmon fisheries and aquaculture sites indicated that 66–327 harbour seals were shot each year between 1994 and 2002. Matrix models and estimates of potential biological removal indicate that this level of shooting is sufficient to explain observed declines. Nevertheless, uncertainty over the number and identity of seals shot means that other factors such as changes in food availability may be contributing. Recent conservation measures markedly reduced the recorded levels of shooting in 2003 and 2004. In 2005, a coordinated management plan was developed to protect salmon fisheries interests while minimizing impacts on local seal populations. Comprehensive monitoring of future population trends and improved regulation of culls are now required to provide more robust assessments of the impact of human persecution on harbour seal populations in the Moray Firth and in other parts of the UK.