In order to investigate the response of mycorrhizal fungi to different kinds of fungicides and phytohormone balance in soybean, the present study was carried out during 2008-2009 at Research Site of Azad University of Karaj branch as factorial based on randomized complete block design with two factors and four replications. Treatments were all combination of arbuscular mycorrhizal fungi species in four levels (Glomus mosseae, G. etunicatum, G. intraradices, control) and four fungicides [control, benomyl, Nano-silver and biologic (Bacillus subtilis)]. The results indicated that fungicides and mycorrhizal species had significant effect on phytohormons and mycorrhizal colonization. The mutualistic interaction between arbuscular mycorrhiza (AM) fungi and fungicide had significant effect on phytohormone changes. Gibberellin (GA), Auxin (AX) and cytokinin (CK) considerably increased in response to three species infection. G. intraradices inoculation brought about the largest increase (35.33%) in mycorrhizal colonization in comparison with control. The level of phytohormons significantly decreased in comparison with control by fungicide treatments. Mycorrhizal colonization decreased 44.12% by using Bacillus subtilis as biofungicide. AX, GA and CK concentrations decreased in AM-colonized plant when subjected to different fungicide treatments. Biofungicide had the most consistent effects towards G. intraradices and CK is found at about 2% higher in this treatment versus nonfoungicide-mycorrhizal treatment. AX, GA and CK tended to decreased 53.58%, 63% and 85.23% by inhibition effects of benomyl on G. etunicatum infection in comparison with nonfungicide control. By using nano-silver, G. mosseae showed more susceptibility than the other species. In conclusion, stimulating of phytohormons synthesis by mycorrhizal association decreased under fungicides stress.