The genus Gnathophis differs from other genera of Congridae in having a moderately blunt and rounded tail tip and a slightly hardened tail extremity. The fleshy tip of the snout extends distinctly forwards beyond the intermaxillary teeth. A longitudinal fleshy keel is present on the ventral surface of the snout tip. Currently, two species of Gnathophis have been recorded from Taiwan, G. heterognathos and G. asanoi, whereas G. xenica has subsequently been determined to be a misidentification. In this study, three new species of the congrid eel genus Gnathophis Kaup are described from deep-sea waters off northeastern and southwestern Taiwan, based on 130 specimens. Gnathophis kbalanensis sp. nov. is diagnosed by the combination of blackish dorsal, caudal, and anal fins; 34-36 preanal vertebrae, 42-43 precaudal vertebrae, and 134-137 total vertebrae; 32-35 preanal lateral line pores; and elevated lateral line pores above the pectoral fin. Gnathophis melanurum sp. nov. is distinguished from its congeners by having whitish dorsal and anal fins and a blackish caudal fin; 28-32 preanal vertebrae, 37-41 precaudal vertebrae, and 98+-125 total vertebrae; 29-32 preanal lateral line pores; and elevated lateral line pores above the pectoral fin. Gnathophis nanhaiensis sp. nov. is separable from other species of Gnathophis in possessing whitish dorsal, caudal, and anal fins; 40-42 preanal vertebrae, 47-48 precaudal vertebrae, and 139-143 total vertebrae; 37-41 preanal lateral line pores; and lateral line pores above the pectoral fin that are not elevated. The validities of G. kbalanensis sp. nov. and G. melanurum sp. nov. are further supported by DNA barcoding analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Molecular comparisons additionally indicate that specimens of G. heterognathos (Bleeker) from waters off Taiwan exhibit a maximum intraspecific COI sequence divergence of 1.4%.