Hydroxyl radical (OH), the main atmospheric oxidant at the global scale, is believed to play an important role in the dynamics of dissolved organic matter in the sea. Herein, we provide evidence, on the basis of seven experiments performed in contrasting ecosystems (subtropical NE Atlantic and Antarctic waters), of high fluxes of atmospheric OH into the surface oceanic layer, particularly during afternoon events. The experiments demonstrated a tight negative relationship between phytoplankton abundance and the concentration of OH in surface seawater, with acute cell death during afternoon atmospheric OH influx events. The effect of OH radical was higher for picophytoplankton organisms, with Prochlorococcus showing the highest decay rate and the shortest half-life among the phytoplankton populations habiting the ocean surface layers. Our results provide evidence for a high toxicity of atmospheric-derived OH radical to phytoplankton of the surface layer of the ocean.