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This study investigated the seasonal dynamics of planktonic ciliates, including their cyst production, in a eutrophic coastal ecosystem in the subtropical western Pacific from March 2008 to July 2009. The abundance of planktonic ciliates ranged from 0.2 to 13 ¡_ 102 cells L-1 and cyst production ranged from 0 to 3 ¡_ 104 cysts m-2 d-1 during the study period. The dominant cyst types in this study were Type I and Type II which are similar to Strombidium conicum and Strombidium capitatum, respectively. Cyst abundance changed with inter-day variations in salinity during the warm season (> 24¢XC), leading us to conclude that environmental change in the form of freshwater input contributed greatly to the encystment of ciliate populations and might be the primary factor controlling encystment production.