Recently, a great reduction of sea ice coverage has been reported for the Arctic Ocean during summer. The reduction has been reported to be greater for regions which connect the Arctic with the Atlantic and the Pacific Ocean, respectively. Since the pelagic fauna differs between the Atlantic and the Pacific Ocean, the effects of sea ice loss on the species and, thus, the Arctic ecosystems are expected to be different. However, little information is available on the differences in pelagic community between the Atlantic and Pacific sectors of the Arctic Ocean. In this study, we investigated planktonic copepod abundance, biomass and community structure in the Atlantic and Pacific sectors of the Arctic Ocean, and address their differences.