Biological control of soil-borne plant pathogens is a potential alternative to the use of chemical pesticides, which have already been proved to be harmful to the environment. Several strains of the fungus Trichoderma have been isolated and found to be effective biocontrol agents of various soil-borne plant pathogenic fungi under greenhouse and field conditions. Different application approaches have been used including integration of Trichoderma with reduced doses of chemical agents. Biochemical and molecular biology studies carried out to explore the mechanisms involved in biological control revealed that Trichoderma is a rather specific mycoparasite. Lectins were found to be involved in the recognition between Trichoderma and its host fungi, whereas chitinase is involved in the degradation of the host cell wall. Genetic engineering techniques were employed in order to increase the effectiveness, stability, and biocontrol capacity of Trichoderma spp. as well as other biocontrol agents, such as Pseudomonass spp. and Rhizobium.