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This study evaluated the efficacy of two commercial biocides, i.e. Bio-Zeid (Trichoderma album) and Bio-Arc (Bacillus megaterium) against Fusarium wilt disease of tomato caused by Fusarium oxysporum f. sp. lycopersici (FOL) and F. solani (FS). Application of these biocides as soil treatment significantly (P=0.05) reduced the percentage of the disease severity of tomato wilt caused by both pathogens under greenhouse conditions at growing seasons 2016 and 2017 when compared to the control treatment. Untreated and treated infected tomato plants (Super strain B cv.) with the tested products were subjected to study the alterations in gene expression using protein profile and four different isozymes(esterase, peroxidase, chitinase and Superoxide Dismutase isozyme) systems. Treated tomato plants showed differences in protein and isozymes banding patterns compared to untreated plants. Two new protein bands at molecular weight 47.2 KD and 16.3 KD were appeared in all infected plants treated with Bio-Zeid and Bio-Arc while, not appeared in control plant. This indicates that these treatments were able to induced new protein bands which increase resistance in tomato plants to Fusarium wilt infection. All treatments were able to induced new protein bands patterns which increasing resistance to Fusarium wilt, but treatment with Bio-Arc was the best because it induced the higher numbers of new protein bands. At the same time, new esterase band (EST-5a), peroxidase (PRX-4a), chitinase (Chit-5b) and Superoxide Dismutase isozyme (SOD-1a) bands were detected in all treatments while not appeared in the control.