With land-use (cover) and water quality, the distributional characteristics of epilithic diatom communities were studied with 193 samples from estuaries of Korean peninsula between 2015 and 2016. Of total 394 taxa classified, Nitzschia perminuta (19.6%) and N. inconspicua (14.0%) were the 1st and 2nd dominant species. Using a cluster analysis, the epilithic diatom communities of Korean estuaries were divided into four groups (G1-G4). Ecological characteristics of each group were followed: G1 was located in estuaries of the East Sea, and characterized by high forest land-use and high DO and low nutrients; G2 was the eastern part of the South Sea, and characterized by low turbidity and nutrients; G3 was the western part of the South Sea, and characterized by high agriculture, low electric conductivity and low salinity; G4 was the Yellow Sea, and characterized by high nutrients. The environmental factors having significant correlation with diatom distributions were as follows: TN to G1, turbidity to G2, agriculture to G3, and TP to G4. Moreover, the important factors affecting the occurrence of indicator species were forest land-use for Fragilaria construens var. venter in G1, turbidity for Rhoicosphenia abbreviata in G2, urban land- use and total phosphorus (TP) for Bacillaria paradoxa and Hantzschia amphioxys of G3, and TP and turbidity for N. ovalis and Stephanodiscus invistatus of G4. These results collectively indicate that the distribution of epilithic diatom communities in Korean peninsula was largely effected by water quality and land cover/use.