The apatites (carbonate fluorapatites) in central part of Guizhou Province have been made a thorough study depending mainly on chemical composition, IR spectrum, structural sulfur and carbon isotopic compositions, trace elements and rare earth elements. We find that the microbial organic effects are striking in apatite formation. It is showing by IR spectrum of apatite that the CO32- and SO42- replaced PO42- into structure of apatite. In apatite, δ34S is +34.2‰—42.4‰, δ 13C is 3.63‰-+0.10‰ . According to our study of structural sulfur and carbon isotopic composition, the SO42- and CO32- came mostly from the evolution of microbioaal organism. In stromatolitic apatite, the P2O5 is obviously related with biophile elements. But in general, it is quite different from the non-stromatolitic apatite where P2O5 is not closely correlated with biophile elements. REE and trace elements analyses reveal two different processes for the formation of apatite. One is direct absorption and uptake by bateria and alga. The other is indirect action. i.e. authigenous precipitaion of the apatites near surface of deposition or in pore water. In here, organic matter played an action that might provide energy for releasing phosphorus from-phosphor bearing organic compounds. Formation of phosphorites appears to have a mixed origin of above-mentioned two actions.