A study on the indigenous diatoms was carried out at 103 sites during August 2008 to April 2011 from the marine and the brackish waters in Korea. A fine structure of small-sized diatoms was examined using a light and scanning electron microscopy. Sixty species of diatoms were newly identified and composed of 3 class, 6 subclass, 16 order, 21 family and 39 genus. The detailed nomenclatures, references, photographs and distributions were here reported. Of 60 species, the most frequent species was Tryblionella coarctata appearing 24 times, and 22 times followed by Thalassiosira lacustris, Cocconeis stauroneiformis was 20 times. In the level of genus, Chaetoceros, Parlibells and Thalassiosira were included 4 species, Actinocyclus, Minidiscus and Licmophora were included 3 species. This study will provide the knowledge of the diversity level of diatom in Korea, the knowledge is important on the diatoms for further studies.