A study on the fine structure of the genus Achnanthes species (Bacillariophyceae) is carried out at 92 stations for taxonomic purposes from January 2009 to April 2013 in Korean marine water, freshwater and brackish water. Twelve Achnanthes species are identified based on a variety of taxonomic characters by means of light microscopy and scanning electron microscopy. Of these, seven species, Achnanthes cocconeioides, A. groenlandica, A. javanica, A. kuwaitensis, A. parvula, A. pseudolongipes, and A. yaquinensis, are newly recorded in Korean waters. All 12 species are documented concerning a taxonomic key, description, distribution, seasonality, remarks and photographs. Twenty three Achnanthes taxa are identified in the survey.