Glyptothorax pongoensis, sp. n. is described from the Yongmon River in Nagaland, India. The new species can be distinguished from its congeners in the Indian subcontinent by the following combination of characters: an ovate-shaped thoracic adhesive apparatus with skin ridges present over the entire apparatus, including the subulate-shaped median depression; presence of plicae on the ventral surface of the pectoral fin spine and the first ray of the pelvic fin; W-shaped anterior nuchal plate element; dorsal-fin origin nearer to the snout tip than to the origin of the adipose fin; posterior margin of dorsal spine rugose with 4–5 ridges, tuberculate skin, and nasal barbel not reaching eye when adpressed.