The roots of soybean (Glycine max [L.] Merr.) establish symbiosis with nodule-inducing rhizobia and arbuscular mycorrhizal (AM) fungi. The existing nodules systemically suppress subsequent nodule formation, a phenomenon known as autoregulation. Grafting experiments revealed that some forms of autoregulation are controlled by the shoot. In the present study, we examined shoot-controlled regulation of AM fungal colonization using a reciprocal grafting technique. Ten-day-old seedlings of wild-type soybean cv. Enrei and its hypernodulating mutant En6500 were cut below the cotyledons and the shoots were grafted to self or reciprocal roots. Grafted seedlings were inoculated with Bradyrhizobium japonicum and Gigaspora rosea and grown in a glasshouse for 60 days. The arbuscule abundance of the En6500 (shoot)/En6500(root) graft was 1.5-fold higher than that of the Enrei/Enrei graft. In grafts between Enrei and En6500, an increased arbuscule abundance was detected only when En6500 was used as the shoot. The arbuscule abundance of Enrei/En6500 when Enrei was used as the shoot was comparable to that of Enrei/Enrei. The intensity of AM fungal colonization was lower in Enrei/En6500 than in the other grafting treatments. From the results obtained, we suggest that soybean shoots systemically control arbuscule formation in both AM symbiosis and nodule formation.