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Seasonal variations in the picoplankton community were investigated from June 2002 to March 2004 within the photic zone of Sagami Bay, Japan. The study area was mostly dominated by coastal waters during the warm period (mixed layer water temperature ≥ 18°C). During the cold period (mixed layer water temperature ≤ 18°C), the water mass was characterized by low temperature and high saline waters indicative of the North Pacific Subtropical Mode Water (NPSTMW). Occasionally, a third type of water mass characterized by high temperature and low saline properties was observed, which could be evidence of the intrusion of warm Kuroshio waters. Synechococcus was the dominant picophytoplankton (5−28 × 1011 cells m−2) followed by Prochlorococcus (1−5 × 1011 cells m−2) and picoeukaryotes during the warm period. Heterotrophic bacteria dominated the picoplankton community throughout the year, especially in the warm period. During the Kuroshio Current advection, cyanobacterial abundance was high whereas that of picoeukaryotes and heterotrophic bacteria was low. During the cold period, homogeneously distributed, lower picophytoplankton cell densities were observed. The dominance of Synechococcus in the warm period reflects the importance of high temperature, low salinity and high Photosynthetically Active Radiation (PAR) on its distribution. Cyanobacterial and heterotrophic bacterial abundance showed a positive correlation with temperature. Prochlorococcus and picoeukaryotes showed a positive correlation with nutrients. Picoeukaryotes were the major contributors to the picophytoplankton carbon biomass. The annual picophytoplankton contribution to the photosynthetic biomass was 32 ± 4%. These observations suggest that the environmental conditions, combined with the seasonal variability in the source of the water mass, determines the community structure of picoplankton, which contributes substantially to the phytoplankton biomass and can play a very important role in the food web dynamics of Sagami Bay. [ABSTRACT FROM AUTHOR]