Elevated temperatures differentially affect the development of cultivated microfungal assemblages, including species potentially pathogenic for humans, in various natural and anthropogenic soils. For that reason it is important to know whether the relative abundance and diversity of fungal pathogenic species increase at elevated soil temperatures. We compared successional changes in microfungal species diversity in natural (Histic Leptosol, Umbric Albeluvisol) and anthropogenic (Urbic Technosol) soils of the boreal zone of European Russia at temperatures of 10, 20, 30, and 35°С, and at a water holding capacity of 60% using the soil dilution plate method. The greatest fungal diversity was detected at the lowest but common temperature (10°C) in the investigated regions. The most significant changes in the diversity of fungal assemblages in the process of succession occurred at 20°C. Elevated soil temperatures (30 and 35°С) induced a drastic decrease in species diversity compared with what was observed at 10°C.During the successions, microfungal assemblages in both types of natural soils had the most pronounced differences in species composition at minimal (10°С) and maximal (35°С) soil temperatures. In the anthropogenic soil, microfungal communities at varying stages of succession were more similar at different temperatures, with the exception of the final stages of succession at the highest temperature of 35°C. Independently of soil type, elevated temperature increased (up to 40–90%) the relative abundance of potentially pathogenic microfungal species dangerous for humans. Potentially pathogenic Aspergillus fumigatus was dominant in the natural soils, while Scedosporium aurantiacum dominated in the urban soil. Elevated soil temperatures in combination with high humidity due to climate warming may drastically accelerate the development of potentially pathogenic microfungal species.