Macrognathus guentheri can be distinguished from Macrognathus albus by the following characters: body with distinct bars or marblings (vs. absent in M. albus), head shorter (14.1-6.3 % SL vs. 16.6- 17.4) and less deep (39.5-42.2 % HL vs.43.0- 48.6), body wider (7.0-7.5 % SL vs. 5.7- 7.1), pre dorsal (21.1-24.0 % SL vs. 26.9-28.4) and pre anal (56.0-61.6 % SL vs. 61.5-67.4) distances shorter, eyes are widely set (inter orbital width 10.5- 12.0 % HL vs. 6.3- 6.8), snout shorter (37.2- 41.1 % HL vs. 42.8- 48.4) and anal fin with 62-75 soft rays (vs. 56-62); irregular blotches absent on the mid dorsal side and extending a little to upper lateral side stretching from the opercle to caudal base (vs. present); dorsal spines comparatively longer and prominent (vs. short and partly hidden under skin); spinous part of dorsal fin originating just behind the end of pectoral fin (vs. originating considerably behind the end of pectoral fin); and preorbital spine present (vs. absent) (Ref. 97143).