Current work describes the changes in fungal pathogen componence of the Fusarium species found in DNA samples from winter wheat grain using nested-PCR and species-specific primers. DNA was extracted from grain of three soft winter wheat cultivars (Moldova 66, Moldova 614, Kuialnik) right after harvesting in 2021 and after storage under room conditions and in storage facility untill April 2022. Using molecular methods of analysis it was found that Fusarium fungi accumulated continuously in grain of all cultivars both during storage under low temperature and uncontroled air humidity and under room conditions compared to grain samples after harvesting. Prior to kernel long-term storage after harvesting special seed-preparation protocols should be applied (thermal treatment, ozonization, aromatherapy and others), because fungi`s propagation continues even after seed harvesting, micelium`s vitality and fungi`s reproductivity persists.