Background: Bacterial endophytes live inside the plant tissues and are known to play a crucial role in the functioning of host plants by influencing their physiology and development. Moreover, this group of bacteria could produce secondary metabolites to suppress plant pathogens and also produce compounds to promote plant growth. Methods: In this present study, Bacillus amyloliquefaciens was isolated from Oryzae officinalis and screened for antifungal activity against rice sheath blight pathogen, Rhizoctonia solani by dual culture assay. The secondary metabolites produced during the interaction of B. amyloliquefaciens with R. solani were characterized with pathogen-inoculated control and antagonist inoculated control through Gas Chromatography-Mass Spectrophotometry (GC-MS). Result: The isolated Bacillus amyloliqufaciens displayed antagonistic activity against Rhizoctonia solani which showed a 63% inhibiton in the mycelial growth of R. solani over control. Analysis of secondary metabolites from the zone of inhibition, confirmed the presence of unique biomolecules including -Propanamine, N,N,2-trimethyl, 1(2H)-Naphthalenone, 3,4-dihydro-6,7-dimethyl, Diethyl Phthalate, Dichloroacetic acid tridecyl ester, Hexadecen-1-ol trans-9, Glycine N-(N-glycyl-L-leucyl) and 2,6,10-Dodecatrien-1-ol, 3,7,11-trimethyl of antifungal and antimicrobial nature.