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Ciliates are important components in planktonic food webs, but our understanding of their community structures in different oceanic water masses is limited. We report pelagic ciliate community characteristics in three seas: the tropical West Pacific, the Bering Sea and the Arctic Ocean. Planktonic ciliate abundance had bimodal-peak,surface-peak and DCM (deep chlorophyll a maximum layer)-peak vertical distribution patts in the tropical West Pacific, the Bering Sea and the Arctic Ocean, respectively. The abundance proportion of tintinnid to total ciliate in the Bering Sea (42.6％) was higher than both the tropical West Pacific (7.8％) and the Arctic Ocean (2.0％). The abundance proportion of small aloricate ciliates (10-20 μm size-fraction) in the tropical West Pacific was highest in these three seas. The Arctic Ocean had higher abundance proportion of tintinnids in larger LOD (lorica oral diameter) size-class. Proportion of redundant species increased from the Arctic Ocean to the tropical West Pacific. Our result provided useful data to further understand ecology roles of planktonic ciliates in different marine habitats.