Abstract For the first time, mycological analysis of dust, including assessment of opportunistic fungal species, was carried out for the urban ecosystems of air, vegetation, and paved surfaces in different climate areas (the cities of Murmansk and Moscow). The combined effect of environmental factors (climate, functional zone, and substrate type) on qualitative and quantitative parameters of micromycete communities was assessed using MANOVA and cluster analysis. It was found that the abundance of culturable mycobiota in the air, on tree leaves, and on paved surfaces was lower in Murmansk than in Moscow. In both cities, approximately a half of fungal species were opportunistic pathogens. The relative abundance of opportunistic fungi of the BSL-2 group was higher in the air of the traffic zone in both cities and of the residential zone in Moscow. In the residential and traffic zones of Moscow, the most abundant species in the air in on the road dust were Aspergillus fumigatus and A. niger, while in Murmansk communities were dominated by members of the genera Cephalosporium, Scopulariopsis, and Trichoderma, which are less pathogenic for humans. The most significant factors affecting the abundance and species diversity of micromycetes, including opportunistic fungi, were the substrate type (air, leaves, or paved surfaces) and the climate, while the effect of the functional zone was not significant. The recreation zones of cities located in different climate regions are the most favorable for humans due to lower abundance of opportunistic fungi in the air and to lack of micromycetes of the BSL-2 and BSL-3 groups. However, the abundance of potentially pathogenic species on the surfaces of leaves and roads in this zone was higher than in the air. Therefore, it can be recommended that city residents minimize their contact with the leaves surface and road pavements, which is especially relevant for toddlers, so as to diminish the probability of encountering opportunistic mycobiota that potentially represents a health hazard.