The results presented in this paper have been obtained during a three-year experiment (from the second cycle of four-year trials set up in 2004) established in Bałcyny. The following crops were grown in succession: potato, fodder barley, winter oilseed rape and winter wheat. The fertilization treatments included: mineral NPK, FYM and organic fertilization with composted and dried sewage sludge and composted municipal waste. Treatments without soil enrichment or with mineral NPK fertilization were taken for comparison. Farmyard manure and organic fertilizers were applied in two different ways: as a single dose of 10 t ha–1 before planting the potato or in two doses, each 5 t d.m. ha–1, before planting the potato and before sowing the oilseed rape. The effect of the applied fertilizers on assemblages of soil fungi was tested. The fungi were cultured on Martin medium. The fertilizers were determined to have affected the populations of soil fungi. Yeast-like fungi prevailed among the isolated colonies (60-85% of the total isolates). The richest fungal community was obtained from the soil amended with dried and pelleted sewage sludge or municipal green waste compost. However, suppressed growth of pathogenic fungi represented by the species Aureobasidium pullulans, Botrytis cinerea, of the genus Fusarium and Sclerotinia sclerotiorum was observed in the soil amended with natural fertilizers and composts. The growth of pathogens was most strongly inhibited in the soil enriched with a double dose of FYM, composted urban green waste or with dried and pelleted sewage sludge in either of the two application variants. The pathogen-antagonistic fungi, represented by three species of Gliocladium and four species of the genera Paecilomyces and Trichoderma, were more often isolated from the soil fertilized with FYM or organic fertilizers than the unfertilized or NPK-nourished soil. The soil enriched with Dano compost applied in a single rate of 10 t d.m. ha–1 was most abundantly populated by these fungi. Among the remaining saprotrophs, fungi of the genus Penicillium and the orders Mucorales and Sporotrichum olivaceum were isolated.