A study on indigenous diatoms was carried out at 49 sites from November 2008 to December 2012 in the marine and brackish plankton and benthic ecosystem in Korea. The structure of small-sized pennate diatoms was examined by means of light and scanning electron microscopy. Twenty species of diatoms were newly identified and divided into five orders, 18 families, and nine genera in this study. The nomenclature, references, specimens examined, specimen descriptions, photographs, and distribution profiles are reported here. The newly reported pennate diatoms imply several reasons why these taxa have not been recorded previously in Korea and we present the strategy to understand the diversity of diatoms in Korea.