Organofluorine compounds find extensive application in the fields of agrochemicals, pharmaceuticals, materials science, and molecular imaging. Introducing fluorine atoms can provide organic compounds with unique physicochemical properties or improve their biological activity. Although significant progress has been made in the chemical synthesis of fluorine-containing compounds, achieving selective fluorination under mild conditions remains extremely challenging. Introducing biocatalytic approaches in organofluorine chemistry is an important strategy given their high efficiency, selectivity, and environmental friendliness. In this review, we present the discovery of fluorinated natural products and fluorinases, the crystal structure and the directed evolution of fluorinases, with a focus on recent advances in the enzymatic synthesis of fluorine-containing compounds in recent years. It is hoped that this review will help to promote the field of biocatalytic organofluorine compound synthesis.