Although Mn is one of the major impurities in the economic iron ores from the Bahariya Oasis, information on its modes of occurrence and origin is lacking in previous studies. High-Mn iron ores from El Gedida and Ghorabi–Nasser iron mines were subjected to detailed mineralogical, geochemical, and petrographic investigations using X-ray diffraction (XRD), infrared absorption spectrometry (IR), Raman spectroscopy, X-ray fluorescence (XRF), scanning electron microscopy (SEM), and electron probe microanalyzer (EPMA) to clarify the modes of occurrence of Mn in these deposits and its origin. The results showed that the MnO2 contents range between 0.03 and 13.9wt.%. Three mineralogical types have been identified for the Mn in the high-Mn iron ores, including: (1) inclusions within the hematite and goethite and/or Mn accumulated on their active surfaces, (2) coarse-grained and crystalline pyrolusite, and (3) fine-grained cement-like Mn oxide and hydroxide minerals (bixbyite, cryptomelane, aurorite, romanechite, manjiroite, and pyrochroite) between the Fe-bearing minerals. The Mn carbonate mineral (rhodochrosite) was detected only in the Ghorabi–Nasser high-Mn iron ores. Since IR patterns of low-Mn and high-Mn samples are almost the same, a combination of XRD analysis using non-filtered Fe-Kα radiations and Raman spectroscopy could be the best way to identify and distinguish between different Mn minerals.Assuming that both Fe and Mn were derived from the same source, the occurrence of high-Mn iron ores at the base of the stratigraphic section of the deposits overlain by the low-Mn iron ores indicated a supergene origin of the studied ores by descending solutions. The predominance of Mn oxide and hydroxide minerals in botryoidal shapes supports this interpretation. The small grain size of Mn-bearing minerals as well as the features of microbial fossils such as spherical, elliptical, and filamentous shapes of the Fe-bearing minerals suggested a microbial origin of studied iron ores.Variations in the distribution and mineralogy types of Mn in the iron ores of the Bahariya Oasis demanded detailed mineralogical and petrographic characterizations of the deposits before the beneficiation of high-Mn iron ores from the Bahariya Oasis as feedstock for the ironmaking industries in Egypt by magnetizing reduction. High Mn contents, especially in the Ghorabi–Nasser iron ore and occurrence of Mn as inclusions and/or accumulated on the surface of the Fe-bearing minerals would suggest a possible utilization of the high-Mn iron ores to produce ferromanganese alloys.