To study how natural Southern Ocean phytoplankton communities acclimate to rapid fluctuations in irradiance levels that result from deep wind-driven mixing of the upper water column, we measured their fluorescence properties (Fv : Fm, maximum quantum yield of photosystem II; and qN, non-photochemical quenching) and pigment composition. Values of Fv : Fm were low (0.67) throughout the upper mixed layer (UML). Short-term (20-min) exposure to incident surface irradiance strongly reduced Fv : Fm and recovery was slow under subsequent incubation at low irradiance. This suggests that phytoplankton cells are frequently photodamaged when mixed up to the surface from depth. Recovery of Fv : Fm was suppressed when lincomycin was added, inhibiting synthesis of the photosystem II reaction center D1 protein. This indicates that D1 protein repair is crucial in maintaining photosynthetic performance under fluctuating irradiance levels. Regions within the Antarctic Circumpolar Current (ACC) with a deep UML had lower depth-integrated phytoplankton biomass than regions close to the Antarctic continent with a shallow UML. Surprisingly, the depth-averaged light level within the UML in these latter regions was lower than in the ACC. Thus, it appears that photodamage incurred during the high irradiance portion of the vertical mixing cycle, rather than light limitation, controls phytoplankton growth in regions of the Southern Ocean with a deep UML. This concept represents a shift from the widely accepted paradigm that phytoplankton growth in the open Southern Ocean is limited by low levels of light or inadequate iron supply.