The colonization dynamics in trophic-functional structure of biofilm-dwelling ciliate fauna were studied using two methods based on an artificial substratum in Korean coastal waters of the Yellow Sea during April 2007. Polyurethane foam enveloped slide (PFES) and conventional slide (CS) systems were used to collect ciliate samples at a depth of 1 m. The ciliate fauna represented similar colonization dynamics in trophic-functional patterns that were driven mainly by the algivores, bacterivores and non-selectives in both systems. Simple trophic-functional patterns (e.g. algivores and non-selectives) occurred within the ciliate fauna at the initial stage (1–3 days), while complex patterns (e.g. algivores, non-selectives and bacterivores) were established at the transitional (5–7 days) and equilibrium (9–19 days) stages. However, the time in which ciliate fauna reached a stable trophic-functional pattern was shorter in the PFES than in the CS system. Among four trophic-functional types, the algivores and bacterivores significantly fitted the MacArthur-Wilson and logistic models in colonization and growth curves in both systems, respectively. Furthermore, the species richness and diversity of algivores and bacterivores were significantly higher in the PFES system than in the CS. These results suggest that the PFES system was more effective than the conventional slide method for a colonization survey on trophic-functional patterns of biofilm-dwelling ciliate fauna in marine ecosystems.