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In order to clarify the response of phytoplankton community structure to the meso-scale eddies in the South China Sea (SCS),three cruises were carried out,including aiming at a cyclonic eddy (CE) inthe western SCS in early September 2007;three long lived anticyclonic eddies (ACEs) in the basin from 28 July to 7 August 2007;and a Rossby eddy in the northern SCS in January 2010,respectively.