Cyclotella species were collected at 51 sites from July 2010 to June 2013 in Korean coastal waters. A total of five Cyclotella species (C. atomus var. marina, C. baltica, C. litoralis, C. meduanae, and C. meneghiniana) were identified in this study. The diagnostic characteristics for five Cyclotella species are described, focusing on the spacing, position, number of satellite pores of the mantle fultoportula and valve face fultoportula. In addition, we put the salinity ranges of five species of Cyclotella together. Of the five Cyclotella species, C. baltica, C. litoralis and C. meduanae are newly recorded in Korea.