Tomatoes are considered an important commercial vegetable crop and because of its high nutritional value, it is one of the vegetables that accepted by the consumer and for this it is cultivated in most countries of the world. Given the exposure of tomato plants infected by many fungal and viral diseases during the growing season in the field, where he is considered rot diseases are very important fungal roots in economic terms and is responsible for the loss of a large amount of crop yield as a result of these diseases and based on it has been limited to rot diseases of tomato fungal roots by collecting infected from 6 different governorates of Egypt (Beheira, Giza, Ismailiya, Qalubiya, Qena and Sharkiya). It has been isolated 259 fungal isolates causing rot of those samples in the laboratory. Based on the frequency of fungi isolated from infected tomato natural samples in tomato plants fields average was selected twenty fungal isolates representative of the rate of the frequency and places of sampling and races fungal isolates a three isolates of Fusarium oxysporum and Gibberella godonii, two isolates of Alternaria sp., A. solani, A. chlamydosporum and F. chlamydosporum and one isolate of F. semitectum, Rhizoctoina sp., R. solani Camarosporum tassi, Paecilomyces variotii and Sclerotinia sp.and to conduct test of infection on the roots of tomato sound commercial product was sensitive to diseases rot the roots (GF 12) and follow-up development The patients. Three fungi choose to complete a study Alternaria solani, Fusarium oxysporum and Rhizoctonia solani which gave the best results of the infection in the previous experiment. Experimental twenty bioagents against three causal pathogens in vitro and vivo used the five isolates of Trichoderma harzianum, T. hamatum, two isolates from each of T. viride, T. reesei, T. longibrachiatum and T. atroviride and one isolate from each of T. koningii and T. virens. Where he showed antagonism vital objects Trichoderma harzianum, T. viride, T. longibrachiatum and T. koningii a high ability to inhibit most of the fungal growth nurse tested. Exposing selected objects antagonism vital to stimulating doses of gamma rays and purification of the new generations. The separation of the different metabolic compounds from the new generations and to compare compounds metabolic parent generation causes inhibition of fungal pathogens. Application of volatile compounds resulting from T. viride (second generation / 6.5 kGy) to controlling pathogens studied in vivo. Measuring productivity differences between fungi Trichoderma under study for many of the polypeptide where the results showed that the fungus T. koningii (parent strain and first-generation and second-generation) higher productivity for those polypeptide. Resistant pathogens using for polypeptide derived from T. koningii in vitro and vivo. Estimate lytic enzymes (Cellulose, Chitinase and β1, 4glucanase) from fungi Trichoderma under study as proved study efficiency T. harzianum and his generation, the second production of the enzyme Cellulose while gave T. longibrachiatum and his generation, the second high productivity of the enzyme Chitinase was T. koningii and his generation, the second high productivity of the enzyme β1, 4glucanase. Study the efficiency of different enzymes demolition in the inhibition of fungal growth causes rot the roots in vitro and vivo study where results showed inhibition of the enzyme's ability to causal organisms.