Abstract: Soy isoflavone, a kind of plant secondary metabolite, is a group of 3-phenyl derivative synthesized by cinnamyl-CoA.Soy isoflavone is referred to as phytoestrogen, for it reduces blood pressure, alleviates menopausal symptoms and has numerous other features as well.To provide a reference for further research of isoflavone biosynthesis and molecular breeding of soybean with high isoflavone contents, this review focused the research development on the enzymes and genes related to the biosynthesis of isoflavone, and highlighted transcription factors and their genes controlling this biosynthesis pathway based on a brief overview of QTLs influencing the isoflavone contents in soybean.Some questions and future research avenue of this research area were presented as well.