Structural and functional parameters of periphytic ciliate communities were studied for monitoring water quality in Korean coastal waters during April 2007. The PFES (polyurethane foam enveloped slide) system, a modified glass slide method, was used to analyze periphytic ciliate colonization in marine ecosystems. A total of 27 ciliate species were identified using living observation and silver impregnation method with this system. Although the ciliate colonizations had similar species composition, they represented considerable differences in both structural and functional parameters between the PFES system and the conventional slide system. The species diversity, evenness and the colonization rate (G) were distinctly higher, but the time for reaching 90% equilibrium species number (T(90%)) was shorter in the PFES system than those on the naked slides. Results suggest that the PFES system is more effective than the conventional slide method for periphytic ciliate colonization with high species diversity, evenness, and colonization rate in marine ecosystems.