Paenibacillus polymyxa bacteria strain as a surface modifier in a flotation process could remove 64.89% of MnO2 from high manganese iron ore. A concentrate containing 3.7% MnO2, 0.5% SiO2 and 71.30% Fe2O3, with a hematite recovery of 72.46% is produced from a feed containing 8.79% MnO2, 0.49% SiO2 and 67.90% Fe2O3. The bio-flotation results indicated that such type of bacteria is selective for upgrading El-Gedida iron ore from the Western Desert of Egypt. The role of Paenibacillus polymyxa on the surface properties of pyrolusite and hematite single minerals was investigated through zeta potential, FTIR and adsorption measurements.