As a new biocatalytic reaction media,ionic liquids have caused extensive interests because of their special characteristics compared to the conventional organic solvents.In this review,the biocompatibility of ionic liquids was discussed,including the toxicity of ionic liquids to microbial cells and enzymatic activities in ionic liquids.The recent advances on biotransformation in different ionic liquid-containing systems were then summarized,such as biocatalytic reactions in ionic liquid/supercritical carbon dioxide biphasic media,biphasic ionic liquid/water-systems and water-miscible ionic liquids as solvents,respectively.Meanwhile,further study on the application of ionic liquids for bioconversion was also put forward.