A new species of congrid eel, Ariosoma melanospilos sp. nov., is described from two specimens collected as bycatch landings of deep-sea trawlers at Colachel fish landing centre, off Kanyakumari, the southwest coast of India. The new species is distinguishable from all the known congeners in having two spots on both sides of the mid-dorsal temporal region (vs. absent in all congeners) and a wide interbranchial width of 25.0–30.3% head length. The new species resembles Ariosoma meeki (Jordan & Snyder, 1900) in possessing the unique character of two dark patches at the posterior margin of the eye but can be readily distinguished by the presence of a fifth supraorbital pore and three pores as ascending branch of the infraorbital canal behind the eye, three supratemporal pores (vs. absent in A. meeki) and four black spots on the temporal region. Genetic analysis reveals that the new species is closely related to Ariosoma anale (Poey, 1860) and A. meeki forming a clade with a genetic distance of 20.5% and 19.6%, respectively. We also report Ariosoma dolichopterum Karmovskaya, 2015, for the first time from Indian waters with meristic and morphological characters.