Global climate change is predicted to have large effects on the ocean that could cause shifts in current algal community structure, major nutrient cycles, and carbon export. The Bering Sea is already experiencing changes in sea surface temperature (SST), unprecedented algal blooms, and alterations to trophic level dynamics. We incubated phytoplankton communities from 2 Bering Sea regimes under conditions of elevated SST and/or partial pressure of carbon dioxide (pCO2) similar to predicted values for 2100. In our 'greenhouse ocean' simulations, maximum biomass-normalized photosynthetic rates increased 2.6 to 3.5 times and community composition shifted away from diatoms and towards nanophytoplankton. These changes were driven largely by elevated temperature, with secondary effects from increased pCO2. If these results are indicative of future climate responses, community shifts towards nanophytoplankton dominance could reduce the ability of the Bering Sea to maintain the productive diatom-based food webs that currently support one of the world's most productive fisheries.