Mycobiomes of roots of 1–2-year-old Pinus sylvestris L. and Picea abies (L.) Karst. plants in forest nurseries and natural woods were studied using molecular genetic methods. Biodiversity indicators were established (species abundance, dominance index, Shannon diversity index) and comparative characteristics of the studied mycobiomes were provided.It was revealed that the main species complexes of mycorrhizae of juvenile pine and spruce plants were formed by a similar list of fungal species from the genera Wilcoxina, Phialocephala, Helotiaceae, etc. At the same time, natural regeneration was also characterized by monospecies mycorrhiza represented by basidiomycetes from the genera Russula, Rhizopogon, Laccaria. In fungal communities the highest level of species diversity indicators values was observed for Norway spruce (Hmax = 2.6) and Scots pine (Hmax = 2.5) seedlings from forest stands. The leading factor determining the species structure of mycobiomes, both in natural conditions and in nurseries, was local soil-biotic conditions.