The present study has been aimed to ascertain the antimicrobial activity of extracts from B. zeylanica, against various pathogenic bacterial and fungal strains using the agar disc diffusion method and the most probable antimicrobial compound by GC-MS study. The crude methanolic extract of B. zeylanica the range varied from 6mm to 15mm. Of the five column chromatographic fractions, maximum number of pathogens was inhibited by F4 and F5 fractions and the highest activity was exhibited against A. hydrophila (9mm) and the least against V.cholerae 0139 (3mm) in F4 fraction and in F5 against E.coli and S.typhi (9mm) and V.cholerae classical (4mm) respectively. MIC of F4 fraction showed maximum inhibitory zone against A. hydrophila (8mm) at 100mg concentration and at the same concentration in F5 fraction S. typhi and E.coli (8mm) respectively. Effects of crude extracts of B. zeylanica on fungi range varied from to 3mm (P. oxallcium, A. terreus, Trichoderma sp. and Rhizopus sp.) to 6mm (A. fumigatus). Among the fractions, F4 and F5 showed little activity against the tested fungi. The GC/MS study of B.zeylanica reveals the probable antimicrobial compounds such as 2-piperidinone, undecanal, 2-methyl-, 1,2- benzenedicarboxilic acid, diisooctyl ester, 3-hexadecyloxycarbonyl -5- (2-hydroxyethyl) -4- methylimidazolium ion, a-D-mannofuranoside, farnesyl-, trans-a-bergamotene, diethyl phthalate,phenol,2-methyl-5-(1,2,2- trimethylcyclopentyl)-(S), and 2,2-dimethyl-6- methylene-1-(3,5-dihydroxy- 1-pentanyl) cyclohexane-1-perhydrol. Of the five fractions, the number of fractions active was F4 and F5 and A. hydrophila, E.coli and S. typhi were the most susceptible pathogens in concern with the Babylonia extract and the antimicrobial compounds identified by GC-MS were responsible for the inhibition of tested pathogens.