The lower Carboniferous Luzhai and Baping Formations (ca. 359 Ma) of the South China block, Guangxi Province, comprise an ca. 170-m-thick clastic-carbonate succession capped by Mn ore horizons near the town of Longtou. Excellent exposure of the stratigraphic succession provides an unparalleled opportunity to investigate the origin of carbonate-hosted Mn deposits, which are generally understudied. Lithofacies associations suggest inner and middle shelf clastic rocks accumulated with deposition of carbonates on a mesotrophic middle to outer shelf. In the Longtou region, carbonate deposition during marine transgression culminated with the precipitation of high-grade Mn deposits during maximum flooding. Mn ore horizons are composed of amalgamated alabandite-bearing rhodochrosite, Mn calcite, and braunite laminae. Mn carbonates have been largely interpreted as forming in oxic water columns via reduction of Mn oxides by organic matter. However, paragenetic relationships and δ13C values (similar to those of seawater) indicate the Mn carbonates of Longtou were formed during authigenesis by the emplacement of anoxic, Mn-rich water masses on the distal to middle shelf. Such anoxia is interpreted to have shut down the carbonate factory and diminished sedimentation, a prerequisite for the concentration and precipitation of Mn carbonates in pore water. This research supports the notion that areas of the Paleozoic deep ocean were persistently anoxic and periodically tapped by coastal upwelling to produce Mn- and Fe-rich deposits. Application of this emerging ore deposit model to other economically important carbonate-hosted Mn deposits may improve resource exploration.