The contribution of non-loricate ciliate assemblage to the ecological pattern of a ciliated protozoan community was studied based on a 1-year (June 2007–May 2008) dataset collected from Jiaozhou Bay, northern China. Samples were collected biweekly from five sampling sites. Results showed that: (1) the non-loricate ciliate assemblages were the primary components and significantly correlated with the total ciliate communities in terms of species number, abundance and biomass; (2) the ecological pattern of non-loricate ciliate assemblages was significantly related to that of both total ciliate communities and variations in environmental variables; and (3) spatio-temporal variations in biodiversity (richness, diversity and evenness of species) indices of non-loricate ciliate assemblages were significantly correlated with those of total ciliate communities and the environmental conditions, especially nutrients nitrate nitrogen, nitrite nitrogen and soluble reactive phosphorous. These results suggest that the non-loricate ciliates are a primary contributor to the ecological pattern of total ciliate communities and might be used as a potential bioindicator for bioassessment in marine ecosystems.