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Manganese is an element essential for living organisms. Development of industrial technologies and exploitation of mineral resources have led to the release of large amount of Mn(Ⅱ) into the environment, posing a serious threat to human health. Bioremediation can remove the Mn(Ⅱ) from the environment rapidly and effectively without generating secondary pollution, thus received increasing attention. This review summarized the diversity and distribution of Mn(Ⅱ) removal microorganisms and the associated mechanisms, followed by discussing the effect of environmental factors on microbial Mn(Ⅱ) removal. Finally, the challenges and prospects for bioremediation of Mn(Ⅱ) polluted wastewater were proposed.