The Middle Eocene ironstones of the Bahariya Depression consist of four iron ore types: manganiferous mud-ironstone, fossiliferous ironstone, stromatolitic ironstone and nummulitic–ooidal–oncoidal ironstone. The upper surfaces of these sequences were subjected to subaerial weathering and a lateritic iron ore type was formed. The chemical composition of these ironstone types was investigated by means of micro-Raman spectroscopy. Various closely related iron-containing and manganese-containing minerals were detected by means of the above-mentioned approach. The high spatial resolution and sensitivity of this method allowed us to identify minerals that could not be detected by other techniques. Well-preserved organic materials were observed in one type of ironstones. Therefore, using Raman spectroscopy, we were able to provide evidence that the formation of some of the investigated rocks was biologically mediated. The application of Raman spectroscopy is considered a powerful technique for the identification of both organic and inorganic substances in the studied iron ore deposits. Copyright © 2011 John Wiley & Sons, Ltd.