Two strains of Bradyrhizobium japonicum were evaluated with five commercial cultivars of soybean (Clark, Crauford, Davis, Centaur, and Nessen) and one hypernodulating mutant NOD1-3. The hypernodulating NOD1-3 produced 30-50 times more nodules than commercial cultivars either inoculated with B. japonicum strain USDA 123 or RCR 3409. The current experiments were extended to determine if the restricted nodulation of commercial cultivars could be overcome by grafting them to a hypernodulated shoot (NOD1-3). Grafting of NOD1-3 shoots to Clark and Davis roots induced hypernodulation on roots of Clark and Davis but did not enhance nodulation when grafted onto the roots of Cranford, Centaur, and Nessen. The shoots of Clark, Davis, Centaur and Nessen significantly inhibited nodule formation on the root of NOD1-3, while Crauford shoots did not alter nodule fort-nation on the roots of NOD1-3 as compared with self-grafts of NOD1-3. It appears that the shoot of NOD1-3 has the ability to alter autoregulatory control of nodulation of Clark and Davis cultivars, but did not with Crauford, Centaur and Nessen. The results suggested that the regulation of nodulation in soybean cultivars Clark and Davis is controlled by the shoot factors, while the Crauford was root controlled. Reciprocal-grafts between NOD1-3 and Centaur or Nessen indicate that both shoot and root factors involved in regulation of nodulation and the regulation of nodulation did not depend on bradyrhizobial strains. Isoflavonoid analyses from extracts of rafted plants showed that NOD1-3 shoots had markedly higher root isoflavonoid concentrations in roots of both Clark and NOD1-3. The shoot control of hypernodulation may be causally related to differential root isoflavonoid levels, which are also controlled by the shoot. The current work was extended to investigate the effect of application of an isoflavonoid (daidzein) on nodulation and nitrogen fixation of soybean cultivars Clark and Centaur as well as in vitro growth of Bradyrhizobium japonicum. Application of the isoflavonoid (daidzein) significantly enhanced the nodulation and nitrogenase activity of Clark but not of Centaur indicating that this character is not related to isoflavonoids. Therefore, autoregulation in Clark and Centaur plants may be separate events in legume-rhizobia symbiosis and regulated by different kinds of signals. Addition of daidzein to yeast mannitol broth medium promoted the growth of B. japonicum strain USDA 123 and RCR 3409. It seems that this compound is able to help the nodulation of soybean cv Clark by a Brady rhizobium strain. Understanding the signaling pathways between rhizobia and their host plants may allow modifications of this interaction to improve symbiotic performance.