The spatial distribution of planktonic ciliates over the coastal and continental shelf of the East China Sea were investigated using quantative protargol staining. Aloricate oligotrichs and choreotrichs were dominant in terms of species number, abundance and biomass. Ciliate densities varied between 3 and 2688 cells L⁻¹ with higher values occurring in the coastal water and the mixing water than in the Yellow Sea coastal water and the Taiwan warm water. Ciliate biomass exhibited a similar pattern as abundance. A canonical analysis of principal coordinates demonstrated that the spatial patterns of ciliate community structure could be clearly discriminated in different water masses. Diversity parameters showed strong relationships with spatial changes in ciliate communities and might serve as predictors of water mass in future studies. Our findings provide evidence for using ciliate communtiy composition, supplemented with dominant species and diversity parameters, as potential indicators of water masses in complex marine environments.