The Southern Ocean exerts a strong impact on marine biogeochemical cycles and global air-sea CO2 fluxes. Over the coming century, large increases in surface ocean CO2 levels, combined with increased upper water column temperatures and stratification, are expected to diminish Southern Ocean CO2 uptake. These effects could be significantly modulated by concomitant CO2-dependent changes in the region's biological carbon pump. Here we show that CO2 concentrations affect the physiology, growth and species composition of phytoplankton assemblages in the Ross Sea, Antarctica. Field results from in situ sampling and ship-board incubation experiments demonstrate that inorganic carbon uptake, steady-state productivity and diatom species composition are sensitive to CO2 concentrations ranging from 100 to 800 ppm. Elevated CO2 led to a measurable increase in phytoplankton productivity, promoting the growth of larger chain-forming diatoms. Our results suggest that CO2 concentrations can influence biological carbon cycling in the Southern Ocean, thereby creating potential climate feedbacks.