Abstract: After methyl bromide phase out for soil disinfestation, the traditional agriculturalpractice of applying organic amendments into soil has been re-introduced. Organic amendmentshelp in maintaining the fertility, soil structure and productivity of agriculture soils and preventingnutrient losses, but little is known about its long-term effect on soil fungal communities. Thelong-term effect of incorporating organic amendments of two different methods (biofumigationand biosolarization) has been studied by isolation of soil fungi as part of the microbiota in thebeginning and in the end of the growing season during some years in different greenhouses. Noamended soil and methyl bromide were considered as reference treatments. Results showed thatthese relatively new agricultural practices for soil disinfestations, based on environmentallyfriendlytechniques had similar results than the agricultural practice of soil disinfestation withmethyl bromide, particularly at the end of the growing season.