To identify distribution of epilithic diatom assemblages and the relationship betweendiatoms and water chemistry, samples were collected twice a year from 2008 to 2012, from at 6streams in Jeju Island, South Korea. A total of 171 diatom taxa were identified, and Achnantheslanceolata, Gomphonema pumilum, Melosira varians, Navicula minima and Nitzschia palea weredominantly observed. BOD ranged 0.0~1.6 mg L-1, TN 0.230~13.240 mg L-1 (average 4.432 mgL-1), TP 0.020~0.316 mg L-1 (average 0.092 mg L-1), and N/P rate ranged 2.5~178.5. Average ofepilithic algal chlorophyll-a and AFDM were 1.1 μg cm-2 and 0.6 mg cm-2, respectively. Accordingto BOD standard, the water qualities of study area sites were at ‘Good’ level. However, thehealthiness levels assessed from DAIpo and TDI were ‘Fair’ to ‘Poor’.