As with most other deep-sea anglerfishes, Thaumatichthys shows extreme sexual dimorphism with the females much larger and different in morphology from the males. Female Thaumatichthys are characterized by a long, broad, flattened head with enlarged premaxillaries on the upper jaw that overhang the relatively short lower jaw. The premaxillaries are hinged with the skull in such a way that they can be moved down to enclose the lower jaw in a manner similar that of a Venus flytrap. The outer margin of the premaxillaries bear six rows of long, conical, recurved teeth; the teeth in the lower jaw are much shorter. The number and length of the teeth increases as the fish grows.
The distinctive lure of Thaumatichthys is achieved by an "upside-down" orientation of the illicium (the "fishing rod"): its base is embedded in the skin fold connecting the anterior ends of the premaxillaries, and the short illicium projects down and back so that the esca at the tip hangs down from the roof of the mouth. The escal bulb terminates in a pair of forked tendrils and bears varying numbers of lateral lobes and a single curved denticle. The size of the transparent window in the bulb can be adjusted to change the amount of light emanating from the lure.
The eyes are tiny and placed close to the corners of the mouth. There are numerous black papillae with white tips, resembling those of the lateral line (and likely belonging to the same sensory system), inside the mouth. The body is fairly slender and depressed for a deep-sea anglerfish, with a relatively well developed dorsal fin. The fin rays number 4 in the anal fin, 7 in the caudal fin, 6–7 in the dorsal fin, and 14–16 in the pectoral fins. The upper part of the operculum is divided into 5–13 radiating branches. The skin is velvet black or dark brown, with numerous small spines on the lower part of the head and body. The one specimen of T. pagidostomus measured 6 cm long, the largest known specimen of T. binghami measured 29 cm long, and the largest specimen of T. axeli measured 36.5 cm long.
The males are small and slender, with greatly enlarged olfactory organs, long hooked denticles at the tips of the jaws, and no esca. The skin is a uniform dark brown with small spines throughout. As the male matures, the body and head become less deep and the jaws become more prolongated. The largest known male specimen measured 45 mm long.
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