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Picoeukaryotes are important members of the surface ocean microbial community with high diversity and significant temporal and spatial variations in community composition. Little is known about the picoeukaryotic biodiversity and community in the Yellow Sea, where hydrologic conditions are very different with the influence of the Yellow Sea Warm Current (YSWC). Using Illumina high throughput sequencing targeting 18S rDNA, we investigated the composition of picoeukaryotes at a permanent monitoring site in the central Yellow Sea from 2011 to 2013. Alveolata, Stramenopiles, and Archaeplastida were the main super groups found. Prasinophytes were dominant in N-YSWC (not influenced by the YSWC) samples whilst YSWC (influenced by the YSWC) samples were dominated by different groups, such as MALV-II (novel marine Alveolata), MAST-3, MAST-4 (novel marine Stramenopiles), and Dictyochophyceae. N-YSWC samples were grouped together in nMDS (non-metric multidimensional scaling) using the Bray-Curtis method. Distances between each two YSWC samples were greater. Based on indicator operational taxonomic unit (OTU) analysis (IOA), indicator species of the YSWC were represented by Pseudochattonella farcimen, Florenciella parvula within the class Dictyochophyceae, and Phaeocystis cordata within the class Prymnesiophyceae. The findings in our study suggest that picoeukaryotic communities in the central Yellow Sea differ temporally in response to changes in the YSWC. [ABSTRACT FROM AUTHOR]