Modifications to the tillage system and methods of fertilizer application demand investigation and assessment of their impact on microbial communities in cultivated soils. This study used cultivation-based methods to analyze the abundance, composition, similarity, and species diversity of culturable fungal communities in the rhizo- sphere and non-rhizosphere soil under a reduced tillage, rotational wheat-soybean-maize cultivation system. The trial involved application of subsurface mineral fertilization (NPKS), with surface fertilization serving as a reference point. Subsurface application of mineral fertilizers increases the efficiency of nutrient uptake and promotes better plant growth, and reduces fertilizer losses due to leaching and volatilization. It was demon- strated that among the 4 experimental factors tested (plant species, fertilization variant, ecological niche, and years of study), the crop had the greatest significant differential effect on the mycological indices under study. Significantly higher (α=0.05) total counts of culturable fungi in the rhizosphere and soil were recorded under cereal cultivation, i.e., maize and wheat, while the lowest counts were observed in soybean cultivation. Under maize cultivation, the composition and frequency of dominant genera of these fungi significantly differed from those under wheat cultivation, and to a lesser extent under soybean cultivation. In maize cultivation, significant differences were also observed between the rhizosphere and soil in population density distribution of certain species. The similarity in species composition decreased, while species diversity increased as a result of deep application of NPKS fertilizer in maize and soybean cultivation, as well as after surface application in wheat cultivation. Subsurface fertilization significantly increased the overall abundance of rhizospheric fungi, espe- cially in maize. This was particularly evident in 2015 and 2016. In 2015, the abundance of rhizosphere fungi in subsurface-fertilized plots was nearly twice as high (higher NPKS dose) to 2.5 times higher (lower NPKS dose) compared to surface-fertilized treatments. The abundance of these fungi in the non-rhizosphere soil under maize cultivation was twice as high compared to subsurface fertilization. The method and dosage of fertilizer appli- cation did not cause significant differences in the population structure of dominant genera and species. Signif- icant differences in the overall abundance of culturable fungi and the frequency of dominant genera and species populations were observed during the study years. The article discusses the reasons for differences in the overall abundance, composition, and frequency of dominant genera and species of culturable fungi, depending on the experimental factors investigated. Additionally, the taxonomic (composition) and spatial (frequency) structure of these fungi is comprehensively described.