ABSTRACT: Small copepods are important prey for fish larvae in the Kuroshio region off southern Japan. However, revealing entire community structures of small copepods is difficult using conventional methods. We applied a metabarcoding method to size-fractionated community samples of epipelagic copepods (small: 0.1-0.5 mm, medium: 0.5-1.0 mm, and large: 1.0-2.0 mm). Samples were collected from 2013 to 2016 from the shoreward (Kuroshio Slope, KS) and oceanic (Kuroshio Gyre, KG) sides of the Kuroshio Current at 138° E; the results were compared with those in the center of the subtropical gyre (SG). The KS and KG sites showed both spatial differences and seasonal changes, with distinct differences between winter-spring and summer-autumn in each size-fractionated community. Water temperature markedly influenced copepod diversity and community structure, especially in the small size fraction. Warm-water species in the SG intruded into the Kuroshio regions during high-temperature periods, leading to high diversity in summer-autumn. Inter-annual environmental variations influenced by temperature and productivity were evident in KS, leading to clear changes in the sequence proportions of dominant small copepods including Paracalanus sp. and immature stages of the large copepod Calanus sinicus. Immature stages of medium/large copepods formed a substantial proportion of small-copepod communities in the Kuroshio regions (KS: 28.8%; KG: 24.7%; SG: 11.9%; based on average proportions of sequence reads). Because of their ecological importance and sensitivity to environmental changes, monitoring communities of small copepods with high taxonomic resolution may provide further insights into marine ecosystems, including fish recruitment, in the Kuroshio region.