A new aerophilic diatom species, Humidophila manipurensis sp. nov., is described from the Sadu Chiru waterfalls, Manipur, India, a part of the Indo-Burma hotspot region. This species is characterized by having its valve shape slightly inflated at middle, terminal raphe ends that are slightly deflected, round areolae and a central depression. Further, we also recorded Humidophila bigibba from Meghalaya State, Northeast India, and this population is compared with the type population from Indonesia and Chinese populations. Fine structural details of both taxa were examined using light and scanning electron microscopy and compared with morphologically similar taxa in this genus. Addition of new species from this region will further add to the biodiversity richness of the Indo-Burma biodiversity hotspot. Further, this study confirms the presence of H. bigibba for the first time in India. This species has a deep constriction in the middle of the valve which is not found in the populations from the Indonesia and China.