Recently, studies on the influences of physico-chemical properties of water masses on the distribution of Synechococcus have been conducted. In addition, it is known that different types of Synechococcus can be identified based on its phycoerythrin (PE) chromophores, which are phycourobilin (PUB) and phycoerythrobilin (PEB). This study observed the abundance of Synechococcus and its phycoerythrin chromophores based on the excitation ratio of PUB and PEB, and also examined the major environmental factors which influence the distribution of Synechococcus in the East Sea during autumn 2011 and spring 2012. Surface distribution showed that the abundance of Synechococcus in autumn was higher than that in spring (6.5 ± 4.7 × 103 cells ml-1 in autumn and 1.2 ± 0.9 × 103 cells ml-1 in spring) when water temperature was warmer and nutrient level was higher. Vertical distribution of Synechococcus abundance showed sub-surface maxima for both seasons between 10–30 m depth. Surface distribution of the PUBEX:PEBEX ratio was found in a slightly similar range between autumn and spring (0.83–1.45 in autumn and 0.82–1.34 in spring). Vertical distribution of the PUBEX:PEBEX ratio ranged between 0.77–1.57 and 0.82–1.42 in autumn and spring, respectively. This study is one of the very few studies that examined the PUBEX:PEBEX ratio in the natural samples and found three different types of Synechococcus based on its PUBEX:PEBEX ratio: high PUBEX:PEBEX ratios (> 1) in warm surface layers and in the deeper layers for both seasons; low PUBEX:PEBEX ratios (< 1) in the surface layer in autumn; and a few PUB-lacking Synechococcus. The distribution of the PUBEX:PEBEX ratio was clearly associated with temperature and salinity in which a low PUBEX:PEBEX ratio coincided with colder and less saline water, and vice versa.