Steam rustdisease is one of the major wheat threats in the world, prevention of this plant pathogen accidence or reduction of its severity was of importance in this study. The isolated wheat lipopeptide producers' endophytic Bacillus amyloliquefaciens and Bacillus subtilis BMG03 an over co-producer of both lipopeptides plipastatin and surfactin were used for this purpose. The modified strain has been constructed from B. subtilis BMG01(B. subtilis ATCC168 derivative) by the replacement of the P_pps weak native promoter with a constitutive one P_repU originated from the replication gene repU of Staphylococcus aureus. Five Egyptian wheat (Triticum aestivum) cultivars; Sk93, Yacara, Gemiza 5, Giza 157 and Giza 164 [sensitive cultivars] were infected by Puccinia graminis _var. tritici. and treated with living cells and a microbial suspension containing plipastatin and surfactin mixture of tested bacterial strain and endophyticus Bacillii. Both treated and untreated seedlings have been estimated for Copper-Zinc Superoxide Dimutase (SOD) and Catalase (CAT) genes expressions by Real-Time PCR (RT-PCR) as responsible genes involved in the antioxidant defense system. The values of antioxidant enzymes showed elevated values on the plants with symptoms reduction, SOD has shown overexpression values about high two folds in treated and infected seedlings than in infected ones, while CAT expression values were about three folds more in treated and infected seedlings than in infected ones due to the relationship between the systemic resistance induction (SRI) with the involved biosynthetically substrates in antioxidant defense mechanisms.