This article presents the results of the effect of treatment of winter wheat seeds, the Kuyalnik variety, with chlorine-containing reagents (chloride lime and sodium hypochlorite) on the spectrum of fungal pathogens. The nested-PCR analysis with species-specific primers allowed to identify a significant number of fungal pathogen species from the genera Fusarium, Myrothecium, Alternaria, Penicillium and Aspergillus in DNA isolated from wheat seeds of the control and experimental groups. Alternaria alternata, Fusarium spp., F. avenaceum, F. oxysporum, F. verticillioides, F. equiseti, F. sporotrichioides, Penicillium spp. were found in all variants. Fungi of the genera Myrothecium and Aspergillus were not found in any of the analyzed groups of winter wheat seeds. It is shown that treatment with chlorine-containing reagents does not affect the rate of physiological germination of winter wheat seeds (in all 3 groups it was at the level of 97%). The identity of the spectra of fungal pathogens determined in the control and experimental groups of seeds (groups 1 and 2) by nested-PCR proves the localization of the infection inside winter wheat seeds (aleuron layer, endosperm, germ). Insignificant difference in the composition of fungal pathogens in variant 3 (F. equiseti and F. sporotrichioides were not found) can be explained by the less contaminated seeds taken for the sample used for DNA extraction.