The Southern Ocean is a vast net sink for atmospheric carbon dioxide (CO2), with marine phytoplankton playing a crucial role in CO2 fixation. We assessed how changes in the dominant phytoplankton community and net primary productivity (NPP) affected variations in the partial pressure of CO2 in surface water (pCO(2)(sw)) in the Indian sector of the Southern Ocean during austral summer. pCO2sw was negatively correlated with total phytoplankton and diatom abundances, as estimated from pigment signatures, in the zone south of the Antarctic Circumpolar Current; however, pCO(2)(sw) was not correlated with haptophyte abundance. Additionally, a stronger correlation was found between pCO(2)(sw) and total phytoplankton NPP than between chlorophyll a concentration and pCO(2)(sw). We reconstructed pCO(2)(sw) at inter-annual scale using satellite data and assessed the inter-annual variability of air-sea CO2 flux. Over the period from 1997 to 2007, the integrated CO2 fluxes over the study region showed very large variations from a small source to a strong sink. Variations in the integrated CO2 fluxes were also correlated with changes in satellite-derived phytoplankton community in the Indian sector of the Southern Ocean and changes in the dominant phytoplankton community may control CO2 dynamics in the marginal ice zone.