In the mesopelagic and bathypelagic realms of the ocean there is little light from the sun, but light is provided by bioluminescent organisms. Unlike sunlight, which is diffuse, bioluminescent sources are directed, leading to surface reflections from transparent or mirrored animals that can reveal them to predators. Pigment-based camouflage can reduce surface reflection below that of transparent organisms by absorbing >99.5% of light. We assessed this possibility in 18 species of deep-sea fishes from seven orders. Of the 18 species, 16 had ultra-black skin (reflectance <0.5%). Ultra-black skin was found across the entire body in some species (e.g. Oneirodes sp.) but only on parts of the body, such as the gut, in others (e.g. Cyclothone acclinidens). In all 16 species, the skin had a continuous layer of melanosomes just beneath the basement membrane of the epidermis that lacked the unpigmented gaps found in other darkly colored fishes. Additionally, unlike most fishes, there was no reflective collagen between the melanosomes and basement membrane. Using electron microscopy we measured the size and shape of the melanosomes to determine if they exhibited similar geometry to other fishes. We found that the melanosomes in ultra-black fishes were larger and had a higher aspect ratio than melanosomes in other fishes. Computational modeling of melanosome layers confirmed that the melanosome geometry in ultra-black fishes is optimized to reduce reflectance. Compared to layers of typical fish melanosomes, simulated layers of ultra-black fish melanosomes have less than half the reflectance. This reduction in reflectance is predicted by a mathematical model to reduce the sighting distance of these animals by predators up to six-fold, making ultra-black skin a powerful form of camouflage in the deep-sea.