Species in the genus Trichoderma are important as commercial source of several enzymes and as biofungicides/growth promoters. The most common biological control agents of the genus are strains of T. harzianum, T. viride and T. viriens. In this study, sixteen selected isolates of T. harzianum from different land use types in Embu, Kenya were tested for anatognism against five soil borne phytopathogenic fungi (Rhizoctonia solani, Pythium sp, Fusarium graminearum, F. oxysporum f. sp phaseoli and F. oxysporum f. sp Lycopersici) using dual culture assay and through production of nonvolatile inhibitors. Seven isolates were further characterized using RAPD-PCR procedure to determine genetic variability. All T. harzianum isolates had considerable antagonistic effect on mycelial growth of the pathogens in dual cultures compared to the controls. Maximum inhibitions occurred in Pythium sp- 055E interactions (73%).The culture filtrates obtained from Czapek’s liquid medium reduced the dry weight (mg) of the mycelia significantly while those from the potato dextrose broth showed minimum inhibition growth. Pythium sp was inhibited the most compared to other pathogens. Genetic similarities generated using Jacquard’s coefficient of similarity ranged from 0.231 between isolates 055E and 011E to 0.857 between isolates 010E and 015E. The technique of RAPD was efficient in demonstrating the DNA polymorphism in the isolates of T. harzianum tested showing intraspecific genetic variability. Since all T. harzianum isolates evaluated were effective in controlling colony growth of the soil borne pathogens both in dual cultures and in culture filtrates they could be tried as a broad spectrum biological control agent in the green house and under field conditions.