Symphurus bathyspilus, which attains standard lengths up to 121 mm, is described on the basis of 84 specimens collected in deep waters (248–500 m) in the Philippine Archipelago and off Indonesia. This species is characterized by the combination of a predominant 1–2–2 pattern of interdigitation of dorsal pterygiophores and neural spines; 14 caudal-fin rays; 91–100 dorsal-fin rays; 78–87 anal-fin rays; 50–54 total vertebrae; five hypurals; black peritoneum; uniformly bright reddish-brown (freshly captured) to darker reddish-brown ocular side sometimes with faint incomplete cross-bands; uniformly yellowish to straw-colored blind side with numerous small reddish-brown speckles overlying regions of proximal pterygiophores of the blind sides of the dorsal and anal fins; with dorsal and anal fins darker reddish-brown anteriorly, gradually fading to a pale reddish color in their posterior regions; and with the outer surface of the ocular-side opercle yellowish with reddish-brown speckles. Among congeners, the new species is most similar in some meristic features to those of Symphurus woodmasoni but differs markedly in its ocular- and blind-side coloration, in the pigmentation of its dorsal, anal, pelvic, and caudal fins and its yellowish and speckled ocular-side outer opercular surface.