A newly isolated Bacillus subtilis HHT-1 has the ability to oxidize manganese ions. We attempted to immobilize the cells on the microfiltration membrane and remove manganese ions from the raw water as manganese oxides. After subculturing, the broth was filtered with NTF-5200 (pore size 0.2 μm), Nitto, Japan. The filter was set in Nitto Membrane Master RUM-2, Nitto, Japan and used as the bioreactor. Manganese sulfate was dissolved in distilled water to become 1 mg/l or 0.2 mg/l of the final manganese ion concentration, and used as the raw water. The volume of the bioreactor was 10 ml. The flow rate, pressure, retention time of the bioreactor, and circulation frequency were, 0.08 l/min, 0.4 kgf/cm2, 7.5 sec, and 0.04 time/min, respectively. Removal rate of manganese ions rose with increasing cell mass immobilized. The bioreactor was active even at low concentration of initial manganese (0.2 mg/l) and 0.04 mg/l or less of manganese ion concentration in the treated water was obtained.