Cyanobacteria are well known as an important primary producer in aquatic environments. In marine environments, two genera, Synechococcus and Prochlorococcus are exclusively dominant cyanobacteria. Synechococcus are ubiquitously distributed throughout the world’s oceans and especially dominant in coastal waters. Contrary to Synechococcus, Prochlorococcus are dominant in oligotrophic tropical open oceans, account for over 50% of total chlorophyll and photosynthetic biomass [1]. Synechococcus and Prochlorococcus abundance and diversity have been studied across various oceans [2]. Prochlorococcus can be broadly divided in to two ecotypes, high-light (HL)-adpated and low-light (LL)-adapted and HL and LL groups can be further divided into at least 6 clades [3]. Since a description of distinct 10 clades belonging to Synechococcus 5.1 sub-cluster based on 16 S rRNA gene analysis [4], at least eight lineages have been designated [5]. Although much knowledge on their ecology and diversity has been gained in various oceanic regions, studies on distribution and diversity of these cyanobacteria are rare in the north-western Pacific Oceans. In this study, latitudinal investigations of Synechococcus and Prochlorococcus distribution were conducted 4 times from 10oN to 35oN, including various water masses of the north-west Pacific Ocean [North Equatorial current (NEC), Kurhshio current (KC), East China Sea (ECS)]. Synechococcus and Prochlorococcus showed obviously contrasting distribution patterns in the NW Pacific Ocean. Prochlorococcus showed high abundances (avg. 10.0x104 cells ml-1) in NEC and Kuroshio (avg. 7.4x104 cells ml-1) waters. However, the abundances were remarkably low in the ECS (avg. 2.5x104 cells ml-1) or not detected in northern part of the ECS. Contrary to Prochlorococcus, Synechococcus were most abundant (max. 26x104 cells ml-1) in the ECS whereas the abundances were very low (max. 0.04 x104 cells ml-1) in NEC waters. Thus, Prochlorococcus and Synechococcu