There is a growing interest in the use of Mn(II)-oxidizing bacteria to treat Mn-containing metal refinery wastewaters instead of using conventional chemical approaches since the former could reduce the cost of alkaline agents and oxidants to remove Mn(II) as Mn oxides at alkaline pH. The Mn level was found naturally dropped in the industrial metal refinery wastewater treatment system, where the formation of Mn-enriched sludge was apparent. This observation motivated us to investigate the possible involvement of microbially mediated reactions. From the sludge sample, Pseudomonas sp. strain SK3 was successfully isolated and tested for its Mn(II)-oxidation characteristics. Strain SK3 completely removed 100 ppm Mn(II) within 42 hours as birnessite ((Na,Ca,K)0.6(MnIV, MnIII)2O4·1.5H2O) under optimized conditions. Copper ions were found to be an important factor in promoting Mn(II) oxidation. Changes in the Mn(IV)/Mn(III) ratio during bacterial Mn(II)-oxidation indicated the involvement of 2-step one-electron transfer reactions in the formation of biogenic birnessite with Mn(III) as intermediate. Characteristics of strain SK3 were compared with those of a well-known Mn(II)-oxidizing bacterium, Pseudomonas putida strain MnB1. Strain SK3 displayed more robust Mn(II) oxidation capabilities under various severe conditions, showing its ideal characteristics for use in the industrial water treatment process.