SEVERAL fungal diseases affect tomato plants and cause severe economic loss worldwide. Locally isolated fungi were examined for biological control of tomato disease. Pathogenic fungi were isolated from infected tomato plants and identified as Fusarium oxysporum, F. oxysporum, F. solani, F. semitectum, F. equsiseti, Alternaria solani, and A. alternata. Further, non-pathogens, such as Chaetomium globosum, Trichoderma harzianum, Aspergillus tires, and Trichoderma asperelium, were isolated in the rhizosphere from the roots of healthy plants. Both pathogenic and nonpathogenic fungal strains were isolated from two cultivars in Alexandria and Giza Governorates in Egypt. Genetic similarity was assessed using GenBank and PCR (Polymerase Chain Reaction) with ITS1 and ITS4 primers. Efficacy of T. harzianum and C. globosum as biological control agents were evaluated under laboratory conditions for each fungal pathogen. T. harzianum was superior to C. globosum. Changes in protein profiles were noted among treatments. A greenhouse experiment compared the efficacy of the biocide, Bio-Ark, as a model of a bacterial bio-pesticide, and T. harzianum. Both biological agents were assessed against the chemical pesticide, Uniform 390 SE. The T. horizon isolate was most effective based on plant shoot dry weight.