Plants regulate the extent of nodulation and root colonization by arbuscular mycorrhizal fungi (AMF), a phenomenon named autoregulation of symbiosis. We tested AMF colonization in split roots of various soybean genotypes Glycine max (L.) Merr. cv. Bragg, Enrei, Harosoy and Williams, where precolonization of one side of the split-root system by the AMF Glomus mosseae resulted in reduced mycorrhization of the other. AMF precolonization failed to control secondary mycorrhization in the supernodulating Bragg nonsense mutant nts1007 (Q106*), indicating that the GmNARK gene (predicted to encode a leucine-rich repeats (LRR) receptor kinase related to CLAVATA1 in Arabidopsis) is involved in autoregulation of the AMF symbiosis. Here, we tested whether the allelic En6500 nonsense supernodulating mutant (GmNARK K606*, derived from cv. Enrei) and supernodulating mutants of cv. Williams (Nod1-3 and Nod2-4) with yet-undefined genetic lesions exhibit a similar symbiotic phenotype in mycorrhizal split-root systems. Surprisingly, these supernodulating mutants retained their ability to autoregulate AMF. To examine possible differences between two allelic mutants, we determined levels of IAA, abscisic acid, coumestrol, daidzein and genistein in mycorrhizal and uninoculated control roots. Compared with wild-type plants, both mutants showed reduced IAA accumulation in mycorrhizal roots. Roots of cv. Enrei and En6500 exhibited high levels of isoflavonoids not seen in Bragg or nts1007. Taken together, these findings showed that supernodulation mutants, despite a common nodulation phenotype, differ in their ability to autoregulate AMF root colonization. This suggests either that the GmNARK gene product of some mutants is still partially functional (Q106* vs. K606*) or that varietal differences reflected in altered physiological responses suppress the loss of function.