Intact, living roots of Brassica kaber (DC.) Wheeler and Brassica nigra. L. (Brassicaceae) were inhibitory to the germination of spores of the mycorrhizal fungi Glomus intraradices Schenck & Smith and Glomus etunicatum Becker & Gerd. Roots from two similarly non-mycotrophic species, spinach (Chenopodiaceae) and Amaranthus retroflexus L. (Amaranthaceae), had no effect on the germination of spores of G. intraradices. The roots of two out of three mycotrophic species examined were stimulatory to germination of G. intraradices. To test the hypothesis that the inhibition of VAM fungus spore germination by the roots of B. kaber and B. nigra was due to isothiocyanates (mustard oils), lysine, arginine and glutathione were added separately to the nutrient solutions applied to the plants. These compounds were expected to react with isothiocyanates released into the rhizosphere. In one experiment, lysine, arginine and glutathione restored the germination of G. intraradices to control levels for B. kaber, and nearly to the control levels for B. nigra. In a second experiment employing lower concentrations of lysine, arginine and glutathione, germination of spores of G. etunicatum in the presence of B. kaber roots was restored nearly to the levels of controls. In the same experiment, these treatments had no significant effects on spore germination in the presence of B. nigra roots. Lysine and arginine also protected spores of G. etunicatum from in vitro reactions of B. kaber root glucosinolate extract with myrosinase. The involvement of isothiocyanates in the resistance of mustards to VAM fungi is discussed.