The role of algae for sequestration of atmospheric mercury in the ocean is largely unknown owing to a lack of marine sediment data. We used high-resolution cores from marine Antarctica to estimate Holocene global mercury accumulation in biogenic siliceous sediments (diatom ooze). Diatom ooze exhibits the highest mercury accumulation rates ever reported for the marine environment and provides a large sink of anthropogenic mercury, surpassing existing model estimates by as much as a factor of 7. Anthropogenic pollution of the Southern Ocean began ~150 years ago, and up to 20% of anthropogenic mercury emitted to the atmosphere may have been stored in diatom ooze. These findings reveal the crucial role of diatoms as a fast vector for mercury sequestration and diatom ooze as a large marine mercury sink.