Coumestrol (CMS), a coumestan isoflavone, plays key roles in nodulation through communication with rhizobia, and has been used as phytoestrogens for hormone replacement therapy in humans. Because CMs content is controlled by multiple genetic factors, the genetic basis of CMs biosynthesis has remained unclear. We identified soybean genotypes with consistently high (Daewonkong) or low (SS0903-2B-21-1-2) CMS content over 2 years. We performed RNA sequencing of leaf samples from both genotypes at developmental stage R7, when CMS levels are highest. Within the phenylpropanoid biosynthetic pathway, 41 genes were tightly connected in a functional co-expression gene network; seven of these genes were differentially expressed between two genotypes. We identified 14 candidate genes involved in CMs biosynthesis. Among them, seven were annotated as encoding oxidoreductases that may catalyze the transfer of electrons from daidzein, a precursor of CMs. two of the other genes, annotated as encoding a MYB domain protein and a MLp-like protein, may increase CMs accumulation in response to stress conditions. our results will help to complete our understanding of the CMs biosynthetic pathway, and should facilitate development of soybean cultivars with high CMs content that could be used to promote the fitness of plants and human beings. Plants synthesize secondary metabolites to promote their own survival, and some of these compounds have antioxidant or antibiotic effects 1,2. Several lines of evidence suggest that plant secondary metabolites, especially isoflavones, can improve the fitness of both humans and plants. Accordingly, a great deal of research has been conducted on isoflavones. Legume species, including the economically important crop plant soybean, are rich in isoflavones with estrogenic and antioxidant functions 3,4. Within plants themselves, isoflavones play crucial roles in nodulation and nitrogen fixation 5 and defense against environmental stresses 6. In the context of human health, isoflavones, as phytoestrogens, can decrease the risk of menopausal symptoms, breast cancer, osteoporosis, dementia, and cardiovascular disease 7-13. Declining estrogen levels in postmenopausal women are associated with a variety of cutaneous changes, including dryness, wrinkling, poor healing, and hot flashes, many of which can be improved by estrogen supplementation 14. However, the estrogens used in hormone replacement therapy can promote the initiation and progression of breast cancer 15-17. The effects of estrogen are mediated by two estrogen receptors (ERs), ERα and ERβ, which are distributed differently in each tissue 18,19. ERα mediates the breast cancer-promoting effects of estrogens, whereas ERβ inhibits breast cancer cell proliferation and tumor formation 20. Therefore, it has been proposed that dietary or synthetic ERβ-selective estrogens would lack the breast cancer-promoting properties of the estrogens used in hormone replacement regimens 20 .