Abstract. Iron (Fe) can limit phytoplankton productivity in approximately 40% of the global ocean, including in high-nutrient, low-chlorophyll (HNLC) waters. However, there is little information available on the impact of CO₂-induced seawater acidification on natural phytoplankton assemblages in HNLC regions. We therefore conducted an on-deck experiment manipulating CO₂ and Fe using Fe-deficient Bering Sea water during the summer of 2009. The concentrations of CO₂ in the incubation bottles were set at 380 and 600 ppm in the non-Fe-added (control) bottles and 180, 380, 600, and 1000 ppm in the Fe-added bottles. The phytoplankton assemblages were primarily composed of diatoms followed by haptophytes in all incubation bottles as estimated by pigment signatures throughout the 5-day (control) or 6-day (Fe-added treatment) incubation period. At the end of incubation, the relative contribution of diatoms to chlorophyll a biomass was significantly higher in the 380 ppm CO₂ treatment than in the 600 ppm treatment in the controls, whereas minimal changes were found in the Fe-added treatments. These results indicate that, under Fe-deficient conditions, the growth of diatoms could be negatively affected by the increase in CO₂ availability. To further support this finding, we estimated the expression and phylogeny of rbcL (which encodes the large subunit of RuBisCO) mRNA in diatoms by quantitative reverse transcription polymerase chain reaction (PCR) and clone library techniques, respectively. Interestingly, regardless of Fe availability, the transcript abundance of rbcL decreased in the high CO₂ treatments (600 and 1000 ppm). The present study suggests that the projected future increase in seawater pCO₂ could reduce the RuBisCO transcription of diatoms, resulting in a decrease in primary productivity and a shift in the food web structure of the Bering Sea.