The importance of characters of seed coat for taxonomic and systematic research has begun to be appreciated in studies on the subclass Alismatidae recently. The present study examined micromorphological characters of seed coat of six genera,  including 13 species, in the Hydrocharitaceae from China under scanning electron microscope. The characters are described and three types of seed coat are distinguished here according to cell shape of exotesta and endotegmen, sculpture of seed surface and endotegmen tuberculae: (1) Ottelia type, of which the seed coat sculpture is absent, ridged or pilose, cell of endotegmen is polygonal to nearly oblong, and tuberculae sparsely are granulate (e. g. Ottelia Pers. ); (2) Hydrocharis type, of which the seed coat sculpture is verrucate, cell of endotegmen is irregular, and tuberculae densely are baculate (e. g. Hydrocharis L. ); (3) Vallisneria type, of which the seed coat sculpture is verrucate, cell of endotegmen is oblong or nearly oblong, and tuberculae densely are tuberculate (e. g. Vallisneria L., Blyxa Thou et Rich., Nechamandra Planch., Hydrilla Rich. ). There are some differences between genera as well as species in characters such as cell shape of seed coat, sculpture of seed surface and endotegmen tuberculae, and these characters can be served as diagnostic ones for distinguishing tribes, genera and even species in this family.  Micromorphology of seed coats supports Hutchinson’s (1959) and Eckhardt’s (1964) treatments about the tribes Ottelieae and Hydrochariteae.  Vallisneria L., Blyxa Thou et Rich., and Nechamandra Planch. should be placed in the same tribe, and the genus Hydrilla Rich. is closely related to them. In addition, the similarity of verrucae on the seed surface as well as endotegmen tuberculae between the Hydrocharitaceae and Najadaceae may indicate that the two families are closely related.