The state of modern protective plantations in coniferous-deciduous forests of the Non-Chernozem zone is characterized by great heterogeneity. Currently, both protective forest plantations and protective tree plantations are managed by an extensive method, often without taking into account biological relationships in the agrophytocenosis. Successional changes in Aphyllophorales macromycetes (AFMM) at different stages of xylolysis of large tree debris represent a complex biochemical process. The limiting conditions for the active growth of fungal mycelium inside wood include light, access to moisture and air, violations in water transport. As mycogenic xylolysis develops, there is an increase in the biodiversity of AFMM species, which reaches a maximum at stage III–IV. On a large data set of 332 model trees and 3,543 basidiomes of xylotrophic basidiomycetes, the presence of correlations between the settlement on the substrate of various ecological groups of AFMM involved in xylolysis was established. It has also been shown that the fruit bodies of fungi are actively formed under conditions of abiotic stress and their number increases in subsequent seasons. When using AFMM as indicators of the xylolysis stage of coniferous species, it is necessary to take into account that the development of mycelium depends on the structural features of the wood. The course of mycelium development in the trunk cross-section is associated with both the action of external environmental factors and interference processes between species. At the same time, the frequency of basidioma formation and their age are of great importance in field identification.