The manuscript deals with the description of a new genus and species of a deepsea fish parasitic cymothoid. Glyptothoa sagara gen. et sp. nov. is described from the host fish Glyptophidium macropus Alcock, 1894 (Ophidiidae), at depths of 300 to 650 metres from the southwest coast of India. The mitochondrial cytochrome c oxidase subunit I (COI) gene of the species was sequenced and compared with other closely related branchial cymothoid genera. Both morphological and molecular data corroborate the inclusion of this parasitic isopod as a new genus. The adult life stages, such as females (ovigerous and non-ovigerous), males and transitional stage of the new species are described. The species is currently known only from the type locality and the type host. The ecological remarks of the newly described taxon are also provided. The three species of Elthusa Schioedte and Meinert, 1884 are transferred to the new genus Glyptothoa. Glyptothoa is the 43rd genus under the family Cymothoidae and 3rd new genus originally described from Indian waters.