Abstract: In this study, for the management of Basal Stem Rot (BSR) disease sixty endophytic, rhizosphere strains were isolated from coconut, other crops and virgin soils. The strains showed high growth promotion were subjected to Ganoderma mycelium inhibition study in vitro. The strains EPC5 and EPC8 were showed high growth promotion and strong inhibition to Ganoderma pathogen compared to other strains. Both the strains were characterized by biochemical methods and confirmed as Bacillus. The Bacillus ITS region was amplified by specific primers and EPC5, EPC8 showed amplification of 546 bp products in size. Further, the strains were cloned and sequenced, deposited in NCBI, USA. The sequence showed similarity with Bacillus subtilis.