The mineral composition of ferromanganese crusts from Belyaevsky Volcano in the Central Basin of the Sea of Japan has been studied. The crusts have diverse structures and a complex polymineral composition. Along with the previously known todorokite, birnessite, manganite, pyrolusite, and vernadite, we determined rhodochrosite, quenselite, manganosite, hetaerolite, manganotantalite, and tungomelane for the first time. The group of accessory minerals includes magnetite, titanomagnetite, hematite, titanohematite, pyrite, pyrrhotite, galena, monazite, cerianite, and baddeleyite. Copper gold was recognized for the first time in manganese breccia. The origin of manganese minerals was caused by low-temperature hydrothermal fluids, which supplied metals and defined local conditions and intermittent growth of manganese crusts. Sapropel organic matter of siliceous–clayey carbonaceous sediments in the Cenozoic sequences of the deep basin could be a source of metals and the reason for the suboxidizing environments of crystallization of some manganese (manganite, todorokite, and birnessite) and accessory (intermetallics, sulfides, and native elements) minerals.