The present studies aim at determining the antagonistic effect of selected fungi species occurring in the soil under carrot cultivation towards Altenaria dauci (J.G. Kühn) J.W. Groves & Skolko, Alternaria radicina Meier, Drechsler & E.D. Eddy, Fusarium oxysporum E.F. Sm & Swingle, Rhizoctonia solani J.G. Kühn and Sclerotinia sclerotiorum (Lib.) de Bary. The field experiment considered cover crops (oats, tansy phacelia and vetch). The control consisted of traditional carrot cultivation (without cover crops). Statistically, the smallest population of fungi was found in 1 g of soil dry weight after the application of oats, and a slightly bigger – after tansy phacelia and vetch. The largest population of fungi was obtained in the traditional cultivation of carrot. Cover crops contributed to the increase of the population of antagonistic Clonostachys spp., Myrothecium spp., Penicillium spp. and Trichoderma spp. in the soil. Regardless of the experimental treatment, those antagonistic fungi were the most effective in limiting the growth of S. sclerotiorum, A. dauci and A. radicina. The effect of those fungi was a little smaller towards F. oxysporum and R. solani. Oats as a cover crop had the best effect on the antagonistic activity of the studied fungi occurring in the soil environment of carrot.