Mesoscale eddies are found almost everywhere in global ocean. They can last for weeks to months with scales up to over 100 km and play important roles in global biogeochemical cycles. In this study, we analyzed the phylogenetic and pigment type 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. Nutrients pumping enhanced Synechococcus abundance markedly in the upper euphotic layers of CE. High diversity of both phylogenetic clades and pigment types of Synechococcus were discovered in the sampling area, with clear composition difference between CE and ACE. The chromatic acclimating pigment type (PT) 3dA dominated in CE while PT 3dB dominated in ACE. The potential weak chromatic acclimator PT 3eA contributed a significant proportion in both CE and ACE. To better understand the difference of PT composition in CE and ACE, we further investigated the phylogenetic composition of Synechococcus in CE and ACE. Clade CRD 1, which were the main strains in upwelling regions, were dominant in CE, where cooler and nutrient rich subsurface water was pumped to the upper layers. Warm water adapted clade II and clade III dominated in ACE. Our study, for the first time, indicated that chromatic acclimation was important in shaping the vertical profile of Synechococcus community in mesoscale eddies of the subtropical oceans.