The results of the study of the process of bioconversion of the vegetative part of Jerusalem artichoke with fungi of genus Trichoderma asperellum of the strain of «M99/1» and «M99/9» are presented in the paper. It was shown change of the carbohydrate part of the Jerusalem artichoke in the process of biodegradation. It was revealed dynamic of titer of spores and decrease of mass as well as availability of cellulose activity of the studied strains. The carried out tests have clearly demonstrated the expediency of using the vegetative part of Jerusalem artichoke as substrate for the cultivation of fungi of the genus Trichoderma. The obtained results also allowed conducting a comparative characteristic of two new strains which were not studied previously with purpose to identify the most active.