Enzyme-mediated oxidation has been a green and efficient strategy for preparation of derivative chemicals from quinoline and its structural analogues. Herein, we report the progress made to date in enzymatic methods to oxidation of the pyridine moieties of quinoline and its structural analogues 1,2,3,4-tetrahydroquinoline, isoquinoline and 1,2,3,4-tetrahydroisoquinoline, including whole cell- and isolated enzyme-based transformations. In addition, methods to tune the site selectivity of the course of enzymatic transformation are also addressed, in particular the protein engineering approaches.