Since 1997, ocean color satellite images have revealed large-scale blooms of the coccolithophorid Emiliania huxleyi in the eastern Bering Sea. The blooms are often sustained over several months and have caused ecosystem changes in the Arctic Ocean, as well as in the Bering Sea. We examined continental shelf sediment profiles of alkenone, a biomarker for E. huxleyi, covering the past ∼70 years. The alkenone records suggest that large E. huxleyi blooms are a novel feature in the Bering Sea as they have occurred only since the late 1970s. Recent changes in alkenone content were closely related to the 1976–77 climatic regime shift in the North Pacific, implying that warming and freshening of Bering Sea waters promoted E. huxleyi blooms. The production rate of diatoms (total valves in sediment samples), the dominant primary producers in the Bering Sea, also increased during the past several decades. However, the ratio of alkenone content to total diatom valves in the sediments increased as E. huxleyi production increased, suggesting that the increase in the E. huxleyi production rate frequently exceeded the increase in the diatom production rate. Overall, our results indicate a possible subarctic region ecosystem shift driven by climate change.