The quantitative and qualitative parameters of cultivable microscopic fungi communities in various components of urban ecosystems in Murmansk, the largest city in the world above the Arctic Circle, were analyzed and compared with background analogs. The number of microscopic fungi in air, soil, water, and lake sediments within urban ecosystems was more than twice as low as in the background analogs. However, the species diversity of microscopic fungi in urban ecosystems increased by approximately twofold. In soils and lake sediments, there was a low degree of similarity in species composition of microscopic fungi between urban and background ecosystems (Sørensen coefficient of 20–33%), along with changes in dominant species. In urban soils, the dominant species shifted from Acremonium murorum, Sporothrix pallida, and Trichoderma viride to Umbelopsis isabellina in the background forest-tundra. In lake sediments, Paecilomyces variotii dominated in the city, while Penicillium dierckxii was prevalent in the background lake. The mycological hazard levels of urban environmental components ranged from safe in air and water (Im = 0.4–2.3) to hazardous in soil and bottom sediments (Im = 4.8–5.9). The most dangerous microfungal species isolated from urban air, water, and lake sediments were Aspergillus flavus, A. fumigatus, and P. variotii, which are potential causative agents of opportunistic mycoses. These findings may be valuable for organizing the monitoring of mycobiota parameters in Arctic cities.