The effect of long-term systematic application of fertilizers on the mycobiota of meadow chernozem soil in a stationary field experiment (Amur region) was studied for the first time. Information about cultivated soil microscopic fungi is given, an annotated list including 26 species is compiled. It was revealed that the application of nitrogen fertilizers (N30) for wheat against the background of long-term use of fertilizers caused an increase in the total number of soil fungi relative to the control variant by an average of 30–68%, whereas with their aftereffect, a less significant increase in the number of mushroom germs was observed (23–29%). The intervals of the optimal content of macronutrients for the active increase of the pool of microscopic fungi in meadow chernozem soil were determined: phosphorus – 50–65, potassium – 195–210, nitrogen – ≥10 mg/kg with optimal soil moisture of 22–24%. The aftereffect of long-term application of fertilizers, especially organo-mineral fertilizers, as well as the application of mineral fertilizers (N30) directly in the year of the study had a positive effect on species diversity, frequency of occurrence and dynamics of the number of fungal germs in the soil. Negative rearrangements of micromycete complexes as a result of prolonged use of mineral fertilizers in the agrocenoses of meadow chernozem soils were not detected, the introduction of nitrogen-phosphorus fertilizers contributed to a significant decrease in the pool of phytopathogenic fungi.