To understand picocyanobacterial distribution patterns in the northwestern Pacific Ocean, their abundances and genetic diversity were studied using flow cytometry and a barcoded amplicon pyrosequencing approach. At open ocean stations affected by the North Equatorial Current, Prochlorococcus was the predominant picocyanobacteria, and a high-light-adapted ecotype (HLII) made up most of the population. In contrast, at stations in shelf areas of the East China Sea (ECS) and South Sea, Synechococcus was the predominant picocyanobacteria and clade II was dominant. At other ECS stations affected by the Kuroshio Current, both Prochlorococcus and Synechococcus made up similar proportions of the picocyanobacterial community. These results indicate that picocyanobacterial diversity differs among oceanic regions, and that physicochemical properties related to dominant water masses, seem to be important in determining picocyanobacterial diversity.