The genus Amphora is one of the larger genera belonging to the family Naviculaceae and includes about 350 taxa. It is a widespread genus with a few species occurring in freshwater and brackish water, and many species in marine habitats. Members of the genus are clearly distinguished from related genera. The characteristic, strongly dorsiventral frustule has raphe systems which lie close to the ventral margins of the valve. There is no taxonomic revision and clear definition of the genus Amphora based modern taxonomic criteria covering both freshwater to marine species. This study deal with the taxonomy the subgenus Amphora, for freshwater and marine species in Japan. In addition to the characters observable by light microscopy, characters revealed mainly by scanning and transmission electron microscopy, such as raphe system and the shape of dorsal marginal costa, were employed to establish the taxonomy of the taxa considerd herein. Eighteen taxa are recognized in this work. First, each taxon was observed in detail using SEM to expand current knowledge of its fine structure. Taxonomic identification was then confirmed with reference to type material or other historic collections. Among the taxa investigated here, four are new to science, one is a new combination and one is a new name. Ten of the taxa investigated here (Amphora barrowiana (Patr. et Freese) Nagumo comb. nov., A. copulata (Kützing) Schoeman et Archibald, A. hiromuii Nagumo sp. nov., A. inariensis Krammer, A. liriope Nagumo sp. nov., A. macedoniensis Nagumo sp. nov., A. ovalis Kützing., A. pediculus (Kützing) Grun., A. rotunda Skv., A. sibirica Skv. et Meyer) are from freshwaters habitats. Three (A. arenicola (Grun.) Cleve, A. javanica Schmidt, A. libyca Ehr.) are from brackish-water habitats and five (A. gigantea Grun., A. immarginata Nagumo sp. nov., A. marina W. Smith, A. plativalvata Nagumo nom. et stat. nov., A. schmidtii Grun.) are from marine habitats.