Selenium is an essential trace element in life, which plays fundamental roles on human health such as involving in anti-cancer and anti-oxidation defense systems. The reduction of Se(VI) and Se(IV) in microorganisms is a key process in the biogeochemical cycle, but little is known about the molecular mechanisms of toxic Se(VI)/Se(IV) reduction to low or nontoxic Se(0) nanoparticles (SeNPs) under aerobic conditions. In this study, four strains of aerobic bacteria were used as the research materials by using morphological, molecular biology, in vitro enzymology and so on. The main results are as follows. (i) Se(VI) reduction was catalyzed by multiple enzymes of the sulfate reducing pathway in Comamonas testosteroni S44. The Se(VI) was pumped by sulfate transporter into the cytoplasm, where Se(VI) was reduced to Se(IV) and then to Se(0). Trace selenium was converted into organic selenium Se(-II). (ii) It was elucidated that multiple pathways are present for dissimilated reduction of Se(IV) in bacteria, encompassing glutathione reduction pathway in Pseudomonas stutzeri TS44 and Streptomyces sp. ES2-5, a novel selenite reductase SerT in periplasm of C. testosteroni S44, glutathione reductase GorA in strain TS44 and a novel Cr(VI)/Se(IV) reductase CsrF in Alishewanella sp.WH16-1. In conclusion, these results reveal that Se(VI)/Se(IV) are reduced both for assimilation at trace level and detoxification under higher concentrations in bacteria. It is also revealed that diverse mechanisms of Se(IV) detoxification are present in bacteria, even in a strain, including generally glutathione involved mechanism and specially enzyme catalyzed mechanism, and different Se(IV) reductases in various bacteria. Consequently, it is a great challenge to study biological processes of selenium in environment by using marker genes. However, it implies that more mechanisms of Se(IV) reduction need to be elucidated in future.