In the soyabean [Glycine max (L.) Merr.]–B. japonicum symbiosis, genistein has been identified as one of the major compounds in soyabean seed and root extracts responsible for inducing the expression of the B. japonicum nod genes. High combined nitrogen in the growth medium inhibits nodulation and nitrogen assimilation. Two experiments were conducted to test the possibility of overcoming this inhibition by adding genistein to the rooting medium and by incubation of B. japonicum cells with genistein. One soyabean cultivar was used in the first experiment, and two in the second experiment. The experiments were conducted in a glasshouse using a completely randomized design with three rooting medium nitrate concentrations (0, 5 and 10 mM) and four genistein treatments. The genistein treatments were 0 (control), incubation of B. japonicum cells with 5 μM genistein, and regular watering with 5 μM or 20 μM genistein. A two way interaction existed in the first experiment, and two and three way interactions existed in the second experiment. Root growth was inhibited by repeated watering with 20 μM genistein. Weight per nodule was greater at 5 mM than at 0 mM nitrate. At 10 mM nitrate watering with genistein resulted in significant increases in nodule dry weight per plant. Shoot nitrogen contents were significantly increased at 5 mM nitrate by genistein incubation and watering with 20 μM genistein. Watering with 5 μM genistein significantly increased nodule nitrogen concentrations at both 5 and 10 mM nitrate. The two soyabean cultivars responded differently to the genistein and nitrate treatments in terms of nodule number, nodule weight, leaf nitrogen concentration and nodule nitrogen content. Genistein could, at least partially, overcome the inhibition of soyabean nodulation and nitrogen assimilation by nitrate.