During an investigation on the diatom communities of volcanic lakes of Northeastern China a new species belonging to the “Cyclotella comta species complex” was observed. This taxon forms relatively large populations in the phytoplankton of Lake Tuofengling Tianchi, a 33m-deep, oligotrophic, crater lake located in Inner Mongolia. In this paper, the valve morphology and ultrastructure of this taxon is described using light and scanning electron microscopy and a new name, Lindavia khinganensis sp. nov., is proposed. A discriminant analysis based on morphological LM and SEM data confirmed that L. khinganensis is distinct from other Lindavia species with a similar morphology such as L. comta (Ehrenberg) Nakov et al., L. radiosa (Grunow) De Toni & Forti, L. balatonis (Pantocsek) Nakov et al., L. praetermissa (Lund) Nakov et al. and L. tenuistriata (Hustedt) Nakov et al. In addition, the seasonal and interannual distribution of L. khinganensis was investigated using sediment trap samples collected over a two-year period. Limnological data from Lake Tuofengling, including water chemistry and temperature recording from a thermistor chain provided complementary information about the ecology of this new species. This species was not found in any other lakes from Northeastern China that we investigated.