Being stratiform or stratoid, the Huangbaishuwan witherite deposit at Ziyang and the Wenyuhe witherite-barite deposit at Zhushan occur in the lower Lower Cambrian siliceous rocks and the orebodies are remarkably controlled by lithological character and petrography. Boron, carbon and oxygen isotopic studies of witherite, barytocalcite and calcite have shown that the carbon, involved in the formation of these minerals, was derived mainly from hydrocarbons and biogenetic gases resulting from degradation, polycondensation and dehydroxylation of bio-organic matter in sediments at the early stage of diagenesis; the boron was a mixture of boron in pore water and that released in the process of degradation of organic matter, with a minor amount of boron from cycling brines in the deep interior of the basin. Boron, carbon and oxygen isotopic studies unanimously demonstrated that witherite was precipitated in this sort of organic carbon-rich pore water medium during the early stage of diagenesis. Extensive occurrence of biodetritus and clastic texture in witherite ores strongly evidenced that Ba2+ was concentrated and settled down in the form of bio-barite on the seafloor as a result of biological processes, thereafter forming the initially enriched orebodies of barium deposits. Biological processes in seawater and early diagenesis in sediments are the major ore-forming mechanisms of witherite deposits in the region studied.