Two new species in the genus Bacillaria, B. sinensis sp. nov. and B. dongtingensis sp. nov., are described from Dongting Lake, China. Both share the linear-lanceolate valve outline and the fault sites (i.e., branching and/or fusion of transapical ribs), the latter a character of the genus. Even though B. sinensis and B. dongtingensis are found at the same specific locality (sympatric), they differ by two characters: (1) the valves of B. sinensis have asymmetrical flanges on both sides of the raphe, while the raphe flange of B. dongtingensis is only on one side of the raphe; and (2) the valves of B. sinensis lack spines on the valve margins while B. dongtingensis has spines on both margins. Bacillaria sinensis and B. dongtingensis both possess two forms of fault sites on the same valves, i.e., they have both branching of transapical ribs and fusion of transapical ribs on the broader side of valve. This feature is not found in other species of Bacillaria, so it is unique. Bacillaria sinensis and B. dongtingensis are the first two species of Bacillaria reported from a typical and ‘normal’ freshwater habitat.