Plant fungal disease control using environmental friendly (agents) compounds is the aim of various studies. Different commercial products are currently available but the selection and characterization of new, more efficient biological control agents still remains an open field of researches. Several new strains of Trichoderma spp. selected in our laboratory proved an increased activity against various pathogenic fungi (Botrytis, Fusarium, Rhizoctonia, Pythium etc). The use of some of these strains in bio-products formulation is conditioned by a good characterization of biological control agents and, by the possibility of monitoring them after the release, 9 new strains of Trichoderma spp. isolated from various sources (soil, vegetal material, seeds) were subjected to molecular characterization by various methods (ITS-PCR, IGS PCR, RFLP). The molecular methods allow to emphasize a possible intra-specific polymorphism in fungi tested strains as well as to study the possibility of identification of some strain-specific molecular markers. The electrophoretic pattern of the restriction fragments shown that tested Trichoderma strains could belong to some different species.