Resumo. Copper is a heavy metal that can have toxic effects on microorganisms and plants. Ectomycorrhizal fungi are able to protect the plant from heavy metal toxicity, but the presence of certain metal concentrations can inhibit the growth of this fungus, damage the mycorrhizal symbiosis and also altering the development of the plants. The aim of this study was to evaluate the effect of copper on soil bacteria and fungus population, as well as the effects on the ectomycorrhizal association in the development of Eucalyptus grandis, Pinus elliottii and Peltophorum dubium seedlings. The survey of the soil microorganism population was carried out in a greenhouse during 60 days and the treatments consisted of applications of copper sulphate (0.7; 0.708; 0.716; 0.724 mg Kg-1) to the soil and to eucalyptus and pinus seedlings. Eucalyptus and Peltophorum dubium seedlings inoculated and not inoculated with Pisolithus microcarpus (Cooke and Massee) Cunn (UFSC Pt 116) received copper levels of 0, 100, 200 and 300 mg kg-1. The height, stem diameter, shoot and root fresh biomass, shoot and root dry biomass and ectomycorrhizal colonization were evaluated at 110 days. Soil bacteria and fungus population were altered by the presence of copper and the eucalyptus and pinus seedlings were not affected by copper addition. The inoculation of the eucalyptus and canafístula seedlings with isolate UFSC Pt 116 favored the height of the plants and the development of shoot and root fresh biomass. According to the results, canafístula was able to form an ectomycorrhizal association with the isolate tested. The eucalyptus and canafístula seedling development was inhibited by copper following inoculation with the UFSC Pt 116 isolate.