Several sub-Antarctic penguin populations have exhibited decreasing trends in the last 5–20 years. At Iles Kerguelen, the gentoo penguin (Pygoscelis papua) has decreased by approximately 30% over the last 15 years. This decrease is likely to be related to reduced food availability for this coastal species. We discuss this decrease with regard to the impact of overfishing and to the potential effects of climate changes on marine food webs.