The introduction of genetically modified (GM) plants in agroecosystems raises concern about possible effects on nontarget species. The impact of a tomato line transformed for constitutive expression of tobacco β‐1,3‐glucanase and chitinase on indigenous nonpathogenic fungi was investigated. In greenhouse experiments, no significant differences were found in the colonization by arbuscular mycorrhizal fungi. Diversity indices computed from over 20 500 colonies of culturable rhizosphere and phyllosphere saprotrophic microfungi, assigned to 165 species (plus>80 sterile morphotypes), showed no significant differences between GM and wild‐type plants. Differences were found by discriminant analysis in both the rhizosphere and the phyllosphere, but such effects were minor compared with those linked to different plant growth stages.