Background: A large number of bioactive compounds are produced by neem tree (Azadirachta indica). The association between the neem tree and endophytes is not well explored in West Malaysia. Endophytes are the organisms that live inside the medicinal plants and produce bioactive compounds of medicinal importance. The present research work has been carried out to harness significant biocontrol activity showing endophytic bacterial strains. Methods: Screening for bacterial endophytes was performed by using surface sterilisation method. Sterile explants were placed on nutrient agar plates and incubated at 37oC. Plates were observed for the presence of endophytes surrounding the explants. The bacterial endophytes were identified microscopically by Gram staining protocol and molecular characterization was performed by amplification of 16 S rRNA and sequencing. Result: Twelve endophytic bacterial strains isolated in which, only two bacterial strains were found significant in terms of bio-control activity. Therefore, these two bacterial strains were selected for further study. The 16S rRNA amplification and phylogenetic tree construction of endophytic bacterial strains (101 and 201) confirmed that these bacterial strains are closest with Bacillus cereus and Bacillus megaterium strains.