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°C), 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.