•The mineralogy of the Upper Cretaceous Duwi phosphorite deposits were investigated.•Carbonate apatite was the only P-containing mineral detected in the investigated samples.•Apatite is usually associated with CaSO4 and seldom with CaCO3 in the studied samples.•Calcium sulfate and goethite are products of diagenesis and weathering.•The formation of the phosphorite deposits took place in marine environment.The mineral composition of the Upper Cretaceous Duwi phosphorite deposits and underlying Quseir Variegated Shale from Safaga district, Red Sea Range, Egypt, was investigated by dispersive and Fourier transformed Raman spectroscopy. The only phosphorous containing mineral detected in the phosphorite deposits was carbonate fluorapatite. Often carbonate fluorapatite appears associated with calcium sulfate and seldom with calcium carbonate in the investigated samples. Iron is present in the form of goethite and pyrite in the phosphorite layer, while pyrite, marcasite and hematite were identified in the Quseir Shale samples. Also, a high amount of disordered carbon was detected in the black shale layers. The Raman results confirm the hypothesis that the formation of the phosphorites took place in a marine environment. During the formation of black shale, the redox conditions changed, with the pH reaching values of 4 or even lower. Diagenetic and weathering transformations had taken place in the phosphorite deposits, calcium sulfate and goethite being products of these types of processes.Graphical abstract