The Southern Ocean (SO) stores over 40% of anthropogenically derived CO2 and is the world’s largest High- Nutrient Low-Chlorophyll (HNLC) region, where the scarcity of trace metals such as iron (Fe) drives SO phytoplankton composition and biomass build up. As dissolved manganese (dMn) concentrations in the Atlantic sector of the SO are very low (0.04 nM), it was hypothesized that phytoplankton growth may not be limited by Fe only, but also by Mn availability. Our Fe-Mn bottle amendment experiments with two natural phytoplankton communities of the Drake Passage show that only some members of the phytoplankton community were Fe-Mn co-limited, including the biogeochemical important diatom group Fragilariopsis and one subgroup of picoeukaryotes. On the other hand, growth of the ecologically relevant haptophyte Phaeocystis antarctica was significantly inhibited when Mn was added alone. Hence, Fe-Mn availability is a key factor for shaping SO phytoplankton community structure with important implications for the efficiency of the biological carbon pump.