A new species, Epithemia agharkarii sp. nov., is described from the Mula River, Western Ghats, India. The new species is described based on light and scanning electron microscopy; it is characterized by having lanceolate to slightly elliptical valves with rounded apices and being 16–38 µm long and 12.5–17.5 µm wide. Based on morphology, especially the atypical position of the raphe, it is similar to E. reicheltii. The new species is differentiated from the latter by the valve outline, shape of the apices, specific position of the raphe and breadth. We discuss the possible phylogenetic position of these two taxa and recent proposals related to the classification of Rhopalodia and Epithemia.