Identification of common signals of nodulation control among legume species will facilitate progress in enhancing symbiotic nitrogen fixation of legumes in sustainable agriculture system. Grafting experiments between soybean and common bean were carried out to evaluate whether a common shoot signals control the expression of hypernodulation among the tow species. Grafting of a hypernodulating soybean mutant NOD1-3 shoots to three cultivars of normally nodulating common bean roots resulted in hypernodulation on roots of three tested cultivars of common bean. The shoot control of hypernodulation may be causally related to differential root isoflavonoid levels, which are also controlled by shoot factors. Isoflavonoid analysis from root extracts of grafted plants showed that NOD1-3 shoots had markedly higher root isoflavonoid concentrations in roots of both NOD1-3 and common bean cv. Adzuki compared with self-grafts of common bean Adzuki. Exogenous application of daidzein, genistein, coumestrol, glycitein and in combination at concentration of 10 µmol to the nutrient solution significantly increased the nodule numbers of common bean cv. Adzuki. Therefore, the control of hypernodulation expression by isoflavonoid signal molecules translocated from shoot is common among legume species.