Seed inoculation by means of mycorrhizal fungi can alleviate the side-effects of fungicides on production of crops and their yields. An experiment was conducted in 2009 at the Research Field of Islamic Azad University, Faculty of Agriculture, Mahdasht, Karaj. In order to investigate the influence of different kinds of fungicides on colonization of mycorrhizal species and on grain yield in soybean, a factorial experiment on the basis of a completely randomized block design of two factors and four replications was carried out. The first factor was VAM fungi species at four levels of: control, Glomus mosseae, G.etunicatum, G.intraradices. The four fungicide treatments consisted of: control, benomyl, nanosilver as well as biologic (Bacillus subtilis). The results indicated that the most suitable species to increase root colonization (35.33%) in soybean symbiosis was G.intraradices. Grain yield also increased (35.5%) with this species and with nanofungicide application. Biomass recorded the highest (5688 Kg/ha) in a combination of G.intraradices and nanofungicide. Through inoculation of any species of AM with Benomyl, the number of pods, grain and biomass decreased in comparison with control. None of the fungicides exerted any negative effect on grain yield when in combination with any of the species of mycorrhiza.