Phytopathogenic micromycetes are a significant factor reducing the quality of planting material intended for reforestation activities. In this regard, scientific interest is focused on the application of methods for the early diagnosis of pathogens affecting the planting material. This paper presents a detailed analysis of the results of molecular genetic diagnostics of planting material of Pinus sylvestris L. and Picea abies L. Karst. cultivated in forest nurseries of the Arkhangelsk region. The age range of the studied seedlings and seedlings of Picea abies ranged from one to five years, and of the Pinus sylvestris – from one to four years. The diagnosis was performed using seven genusand species-specific primers, each of which provides amplification of a specific marker region of the genome of the pathogenic micromycete. The following phytopathogenic organisms were identified during the study: Fusarium Link, Phoma Sacc., Cladosporium Link, Heterobasidion annosum (Fr.) Bref., Lophodermium seditiosum Minter, Staley & Millar and Lophodermium pinastri (Schrad.) Chevall. Patterns have been established between the frequency of occurrence of identified pathogenic micromycetes, depending on the age of the planting material and its breed. Phytopathogenic organisms colonize the planting material already in the first year of life. At this time, the most dangerous pathogen of the genus Fusarium is identified for seedlings. In the second year of plant life, there is a oneand-a-half-fold increase in the number of pathogens. In subsequent years, the pathogenic load on plants decreases. It was also noted that Pinus sylvestris seedlings are populated by a large number of pathogenic micromycetes.