A new medium-sized species of Hippodonta (Bacillariophyceae) is described from Lake Qinghai, China. The morphology and ultrastructure of Hippodonta qinghainensis sp. nov. are described using light and scanning electron microscopy. This new species is compared with similar species of Hippodonta using conventional and geometric morphometric analyses. Hippodonta qinghainensis can be separated from the other species of Hippodonta by a unique combination of characters that include an elliptic-lanceolate to rhombic-lanceolate valve shape, non protracted apices, the absence of fascia, relatively coarse, uniseriate striae and the presence of two rows of lineolae around the valves apices.