The development of detection and quantification systems for Fusarium spp. is time- consuming. It is, therefore, necessary to develop specific detection methods for this genus to facilitate monitoring of the environment and food for the presence of Fusarium spp. as a potential toxinogenic agent in food. The aim of this work was to find the most effective pre-isolation against self-isolation of DNA from food micromycetes, and then to identify Fusarium spp. at the genus level. By measuring the concentration and purity of the extracted DNA, isolation with pre- isolation, which involved the action of proteinase K and ultrasound on cells of the micromycetes examined, was demonstrated to be most effective.