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To understand the importance of picoeukaryotes in the biogeochemical cycle in the subtropical Kuroshio Current, a year‐round survey of the hydrography and the distribution of picoeukaryotes were conducted in four oceanographic cruises from October 2012 to July 2013. In comparison with other seasons, the highest abundancy of photosynthetic picoeukaryotes, with concentrations >104 cells/ml, was observed around the eastern boundary of the Kuroshio in the winter. Accordingly, the composition of picoeukaryotes in this cold season was further studied by a metabarcoding analysis of the 18S rRNA gene. The majority of picoeukaryotes comprised Alveolata, followed by Haptophyta and Stramenopiles. Their composition was diverse in the waters affected by the Kuroshio and in the offshore province. For Haptophyta, in contrast to clade A prevailing in the Kuroshio waters, clade B1, which was considered the host of uncultivated diazotrophic cyanobacterium group A (UCYN‐A), appeared only in the offshore area. Similarly, in Stramenopiles, Pseudo‐nitzschia spp. and MAST‐1D, respectively, dominated in the Kuroshio‐influenced and offshore areas. While Alveolata was the most abundant group, the distributions of all lineages were similar. The association between picoeukaryote succession and hydrographic change is yet to be fully understood. Our results will assist future studies on the community composition of picoplankton and their relationship with marine ecology in the region.
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