A newly isolated Aspergillus niger strain containing epoxide hydrolase was used to resolve racemic glycidyl azide and four derivatives to the (R)-enantiomers. After optimization of the biotransformation conditions, (R)-glycidyl azide was produced with good enantioselectivity (e.e.(s) > 95 %, E > 20). The substrate structure, pH, and reaction time were found to have profound influences on the catalytic property of A. niger ZJUTZQ208. Enantiopure glycidyl azide was further utilized to synthesize linezolid in good yield, indicating it is a new and concise synthon for chiral vicinal amino alcohols. Enzyme-substrate docking studies were carried out with glycidyl azide to study the selectivity of this strain.