Mesoscale eddies are swirling circulations found almost everywhere in global ocean. Mesoscale eddies are time dependent and can last for weeks to months with scales up to over 100 kilometers, and they play important roles in biogeochemical cycle in oceanic ecosystems. In this study, we analyzed the phylogenetic composition of Synechococcus in a cyclonic eddy (CE, cold eddy) and an anticyclonic eddy (ACE, warm eddy) located in western South China Sea in summer, 2018. Fifteen clades of Synechococcus were detected in the sampling area, with clear difference in clades composition between CE and ACE. Clade CRD1, which were reported to prefer upwelling habitat were dominant in CE, where high nutrient cold water was pumped to the upper layers from the deep layers. Warm water genotype Clade II and Clade III dominated in ACE. In the edge and outside of CE and ACE, large proportions of S5.3 were observed, especially in deep layers. Additionally, four novel clades were identified in this study; some of them accounted for more than 20% in various stations. The phylogenetic position, metabolic characteristics, and ecological roles of these novel clades remain to be further studied.