Abnormal leaf fall (ALF) disease caused by Phytophthora meadii is one of the limiting factors of growth and latex yield in Hevea brasiliensis. Endophytic bacteria reside within the host plant offers very high application potential as biocontrol agents for ALF disease management. Screening of bacterial endophytes from leaf, petiole and root tissues of Hevea brasiliensis was done for the selection of a potent antagonistic isolate against Phytophthora meadii. The most efficient antagonistic isolate was characterized as Alcaligenes sp. The biochemical estimation of antagonist treated plants showed induction of peroxidase activity in leaves. Quantitative PCR analysis confirmed higher activity of lignin biosynthesis promoting class III peroxidase transcripts in antagonist treated plants of Hevea brasiliensis of Hevea brasiliensis. Homology model of the peroxidase class III protein was built from the deduced amino acid sequence and was found to carry 36;helical and 5;beta sheets. Computer aided docking studies of the substrates (p-coumaryl, coniferyl and sinapyl alcohol) with the target proteins showed that the protein-substrate complexes were stabilized by various interactions and proposed that precursors of lignin biosyntheses were preferred by induced peroxidase in Hevea brasiliensis for lignifications. The present study revealed the potential of an antagonistic endophyte for inducing the class III peroxidase involved in defence mechanism in Hevea brasiliensis