A new approach to determining sampling effort for analyzing biofilm-dwelling ciliate colonization was studied in the coastal waters of the Yellow Sea, northern China, from May to June 2010. The optimal sample size for evaluating biofilm-dwelling ciliate colonization increased with shortening exposure time, and can be determined according to the probability of recovering those species with a specified cumulative contribution to communities. More slide-replicates were required at a depth of 3 m than at 1 m to recover equivalent proportions of the ciliate communities. For routine colonization dynamics analyses, 10 slide-replicates (175 cm(2)) were sufficient to achieve a 95% probability of recovering those species with a cumulative contribution of >90% to the ciliate communities at a depth of 1 m. These results suggest that 10 slide-replicates immersed at a depth of 1 m may be an optimal sampling strategy for analyzing the colonization dynamics of biofilm-dwelling ciliate communities in marine habitats.