Greenalite in iron-rich Precambrian sedimentary rocks is widely regarded as a primary mineral that formed in ferrous iron-rich and anoxic conditions. However, primary greenalite has rarely been reported in Phanerozoic rocks, as Phanerozoic oceans are considered to have been more oxygenated and less favorable for greenalite precipitation. Here, we report the discovery of greenalite nanoparticles in the Late Devonian Xialei Mn deposit. Nanoscale (20-1000 nm) euhedral to anhedral greenalite particles occur as randomly oriented crystallites enclosed in microcrystalline quartz crystals within chert-rich Mn and Fe-Mn ores. Greenalite-bearing ores show negative delta 30Si values (avg. -0.5 parts per thousand) close to those of Precambrian iron formations and hydrothermal silica, suggesting a substantial hydrothermal contribution. These characteristics support the interpretation that the greenalite formed in a mixing zone near deep-water vents where Fe2+-rich and SiO2(aq)-rich hydrothermal fluids mixed with seawater to produce gradients in pH and temperature amenable to greenalite genesis. The greenalite nanoparticles then accumulated hundreds of kilometers from this formation zone, being found in continental shelf metalliferous ores formed beneath upwelling zones, as indicated by sedimentologic, stratigraphic, and paleogeographic constraints. The presence of these greenalite-bearing Mn and Fe-Mn deposits on distal shelves (below storm wave base) records a profound regional oxygenstratified water column in South China, characterized by hydrothermal input and anoxic bottom waters. These conditions are reminiscent of Precambrian oceans. Thus, greenalitebearing Mn deposits provide a new archive to track hydrothermal metal fluxes and anoxia in Phanerozoic basins, with potential implications for other Phanerozoic hydrothermal chert and metal deposits.