Impacts of the increasing CO<sub>2</sub> in seawater (i.e. ocean acidification) on phytoplankton physiology may have various and potentially adverse effects on phytoplankton dynamics and the carbon cycle. We conducted a CO<sub>2</sub> manipulation experiment in the Sea of Okhotsk in summer 2006 to investigate the response of the phytoplankton assemblage and dynamics of organic carbon. During the 14-day incubation of nutrient-depleted surface water with a natural phytoplankton assemblage under 150, 280, 480, and 590 μatm <i>p</i>CO<sub>2</sub>, the relative abundance of fucoxanthin-containing phytoplankton such as diatoms and prymnesiophytes decreased with increasing <i>p</i>CO<sub>2</sub>. The amount of DOC accumulation also decreased with increasing <i>p</i>CO<sub>2</sub>, while differences in POC accumulation between the treatments were small and did not show a clear trend with the <i>p</i>CO<sub>2</sub>. Change in the phytoplankton community composition under different CO<sub>2</sub> conditions will alter the organic carbon dynamics as found in the present experiment. Compared to results in the literature from nutrient-replete conditions indicating a potential enhancement of phytoplankton production with elevated CO<sub>2</sub>, the present results indicated a different physiological response of phytoplankton under nutrient-depleted conditions. These results indicate that the continuing increase in atmospheric CO<sub>2</sub> can significantly affect the structure of marine ecosystems and carbon cycle in nutrient-depleted subpolar surface waters.