It is generally accepted that mycobiota diversity in urban greenhouses is poorer than in natural ecosystems, but our knowledge on this field of research is fragmentary. Here, we present the results of a long-term study of aphyllophoroid macrofungi (Basidiomycota) forming fruitbodies on non-native sub/tropical woody and herbaceous plants in the greenhouses of Saint Petersburg, Moscow, and Ekaterinburg botanical gardens located in the hemiboreal vegetation subzone of Eastern Europe. Over 20 years of research, fruitbodies of 58 species of aphyllophoroid fungi have been identified. Fungal species that developed on the wooden structures of greenhouses and building materials made of local wood are discussed separately. The list of fungi on non-native substrates is dominated by saprobes (93.1% of total list) as well as mycorrhizal with basidiomata on plants (8.6%). Phytopathogens have the lowest number (7.0%), and ¾ of species are widespread locally. Non-native plants are dominated by native fungal species (78.9%), while the percentage of non-native species is low (21.1%). In the three surveyed cities, the area of the studied greenhouses is 2.8 ha, and not a single species of fungi has been found twice on the same substrate. Half of the identified species are characterized by a single specimen (29 species/50.9%). Hymenochaete rheicolor was discovered in Russia for the first time and its known distribution is discussed. Only six (Antrodia gossypium, Hyphodontia arguta, Lyomyces sambuci, Peniophora cinerea, Ramariopsis kunzei, and Trechispora farinacea) local species (10.5%) were collected in all the three cities. The α-diversity of mycobiota (mean number of species per site, Shannon Index, and Menhinick Index) in the Ekaterinburg’s greenhouses is 1.2–3.0 times lower compared to suburban forest parks and old-growth natural forests, while β-diversity (Whittaker Index, Jaccard Index, and Morisita–Horn Index), on the contrary, is 2.1–7.7 times higher. With the plants’ age, the probability of detecting fungi on them increases significantly. In greenhouses, phytopathogenic aphyllophoroid macrofungi are collected on woody plants only, but the probability of their development is not related to the plants’ age.