A strict field experiment was conducted in 2004-2007 on grey-brown podzolic soil originatingfrom light silty loam, which was 5.04 in pH, highly abundant in P, moderately abundant in K, Zn, Mn and very poor in Mg. The experiment was established in a randomblock design with four replications. In a four-year crop rotation system, the following sequence of crops was grown: industrial potato, fodder spring barley, winter oilseed rape and winter wheat. The experiment consisted of treatments with farmyard manure and composted sewage sludge (Biohum, Polepszacz, Tyrowo) as well as composted municipal waste (Dano, green waste). The manure and organic fertilizers were applied once (10 t d.m. ha–1) or twice (2⋅5 t d.m. ha–1). For comparison, unfertilized plots (control) and NPK fertilizedplots were used. The phytopathological assays were completed in order to determine the effect of naturaland organic fertilization on the structure of soil fungal communities. In a laboratory, soil samples were made into suspensions of the dilution from 10–2 to 10–4. Fungi were culturedfor 5 days on Martin substrate in Petri dishes at 22oC. The grown fungal colonies werecalculated into g dry mass and inoculated onto agar slabs for later species identification.The results suggest positive influence of fertilization with FYM, composted sewagesludge and composted municipal waste on the chemical properties and biotic relationshipsin soil, i.e. on the growth of fungi which can act antagonistically towards pathogenic species,suppressing at the same time populations of pathogenic fungi. Highest counts of pathogenicfungi were found in unfertilized soil (in the control treatment). The most desirable effect was produced by FYM applied once in a dose of 10 t d.m. ha–1.