A new species of Indo-Pacific grouper is described from nine specimens, 165–391 mm in SL. Epinephelus kupangensis, new species, is similar in appearance to, and has been treated as, Epinephelus amblycephalus (Bleeker, 1857). The two species are both found in deep waters of the Indo-Pacific and have overlapping ranges in eastern Indonesia, and likely beyond. Epinephelus kupangensis, new species, can be distinguished from Epinephelus amblycephalus on the basis of coloration, counts, and measurements. The species is characterized by the following set of characters: dorsal rays XI, 16; anal rays III, 8; pelvic rays I, 5; pectoral rays 18; caudal rays 18; caudal fin rounded; gill rakers 8 16; lateral line scales 48; longitudinal scale series 99; body scales ctenoid; scales on head cycloid and particularly large in size on opercle; orbit diameter 5.1 in head; pelvic fin 4.0 in head; maxillary streak orange; color when freshly dead pale grayish brown with five dark brown bars; orange-brown spots present dorsally on head and at edges and within dark bars.