Population diversity of the species is principal for addressing questions concerning evolutionary processes and developing conservation strategies. Employing model organisms and sensitive DNA markers enables a comprehensive exploration of fungal functional systems and the intricate interplay between the genome and the environment. The cosmopolitan wood-decay fungus Schizophyllum commune is one of them, and widespread allows finding samples in almost all climatic zones, with various extreme environmental factors. The local-scale population research is infrequent because of their unlikely differentiation. Using sensitive genetic markers allows us to identify possible environmental causes leading to genetic differentiation. Our study aimed to determine the differentiation of S. commune local-scale populations with different topographic features and to identify cryptic environmental factors that affect the spread of the fungus's genetic material. The multi-stage study allowed us to establish the most homogeneous location 2 (Feof). Moderate R-values indicate the existence of obstacles to the free spread of the fungal genetic material. The flow direction, the left and right banks of the Dnipro River and altitude affect the spread of the S. commune fungus. These limiting environmental factors also could affect other fungal species with a similar lifestyle cycle. Samples Sc-141 and Sc-208 S. commune significantly influenced on structure of the populations within the research framework, and the movement of descendants occurred from north to south, with the active participation of large waterways (Dnipro River and tributaries).