The diversity and composition of fungal communities inhabiting soils with technologically increased concentrations of natural radionuclides 238U and 226Ra within more than 60 years were studied for the first time. Metabarcoding targeting the ITS region was performed using next-generation sequencing technology. Representatives of Basidiomycota and Ascomycota were dominant in both contaminated and reference soils. Additionally, Mortierellomycota and Mucoromycota were subdominant phyla. In general, no significant differences were observed in alpha diversity of soil fungal communities across different contamination levels and seasons. However, when seasonal variations were disregarded, an insignificant trend toward decreased alpha diversity was noted in radionuclide-contaminated soils. Fungi belonging to Serendipita, Cortinarius, Clavaria, Amphinema, Archaeorhizomyces were more abundant in the communities of contaminated soils. In contrast, Thelephora, Tylospora, Russula, Piloderma, Mortierella, Hymenogaster, Hyaloscypha demonstrated higher abundance in the reference soil. The significant differences in the abundance of certain fungal taxa in the soils of the studied sites mainly involve fungi that are resistant to abiotic and biotic stressors, participate in symbiotic relationships with plant roots and are associated with white rot. These differences likely reflect soil composition and contribute to maintaining the stability of soil fungal communities under conditions of radioactive contamination.