We report the results of a field incubation experiment demonstrating a substantial shift in the taxonomic composition of Equatorial Pacific phytoplankton assemblages exposed to CO2 levels of 150 and 750 ppm (dissolved CO2 ∼3 to 25 μM). By the end of the experiment, the phytoplankton community in all samples was dominated by diatoms and Phaeocystis sp. However, the relative abundance of these phytoplankton taxa differed significantly between CO2 treatments. Taxonomic pigment analysis and direct microscopic examination of samples revealed that the abundance of diatoms decreased by ∼50% at low CO2 relative to high CO2, while the abundance of Phaeocystis increased by ∼60% at low CO2. This CO2-dependent shift was associated with a significant change in nutrient utilization, with higher ratios of nitrate:silicate (N:Si) and nitrate:phosphate (N:P) consumption by phytoplankton in the low CO2 treatment. Despite the significant changes in taxonomic composition and nutrient consumption ratios, total biomass and primary productivity did not differ significantly between the CO2 treatments. Our results suggest that CO2 concentrations could potentially influence competition among marine phytoplankton taxa and affect oceanic nutrient cycling.