Removal of dissolved selenium by D. michiganensis, a iron-reducing bacterium, and effects of dissolved metal elements such as iron, sulfate, and copper were investigated. Selenide that was reduced from selenite (2 mM) by D. michiganensis was gradually removed from the aqueous medium. As the reduced selenide was combined with aqueous iron, it was precipitated as a nanoparticulate iron-selenide. Sulfate and copper negatively affected the microbial selenite reduction, and the copper was especially toxic to the bacterium, inhibiting a microbial removal of dissolved selenite. These results show that it should be carefully biotreated for a selenium-contaminated site considering in situ sulfate or copper distribution and concentration. Consequently, the formation of iron-selenide by bacteria will be an important measure for preventing a long-distance migration of selenium in the subsurface environments.