Thalassiosira species were collected from October 2007 to January 2009 in an attempt to better understand species diversity of the genus Thalassiosira in Korean coastal waters. A total of 5 Thalassiosira species (T. concaviuscula, T. oceanica, T. partheneia, T. simonsenii and T. nanolineata) were identified here. Most species in this study were of small size, and 5 species were recorded for the first time in Korean coastal waters. Using a scanning electron microscope (SEM), we described distinctive characteristics of fine structure that proved to be important diagnostic characteristics for the identification of each species. The most important diagnostic characteristics for Thalassiosira species identification were the marginal strutted processes, the position of labiate processes, and the areolation. The differential characteristics of the species studied were: T. concaviuscula has a double layered external tubes on the marginal strutted processes; T. oceanica shows marginal ridges that are interlinked between the marginal strutted processes; the valve face of T. partheneia is fairly convex and its labiate process is positioned midway between two strutted processes; T. simonsenii is characterized by two labiate processes and somewhat coarse areolae; and, T. nanolineata has several central strutted processes and linear areolation.