The aims of this study were the analysis of the secondary metabolites and evaluation of the antibacterial and antifungal activity of Alternaria alternata. Twenty six bioactive compounds were identified in methanolic extract of Alternaria alternata. The identification of bioactive chemical compounds is based on the peak area, retention time molecular weight and molecular formula. GC-MS analysis of A. alternata revealed the existence of the α-acetyl L-serine, 2(5H)-furanone, 6-oxabicyclo[ 3.1.0]hexan-3-one, D-glucose,6-O-α-D GALACTOPYRANOSYL, DL-arabinose, ƹ-N-fommyl-Llysine, 2-[4-(2-hydroxyethyl) 1-piperazineethanesulfonic acid) (HEPES), thrietol, 2-O-heptyl, 2-deoxy-2- fluoro-1,6-anhydro ß-d-glucopyranose, d-ribo-hexos-3-ulose, Α-D-glucopyranoside, O-α-Dglucopyranosyl-( 1.fwdarw.3)-ß-D-fru, maltose, 4H-pyran-4-one,2,3-dihydro-3,5-dihydroxy-6-methyl, desulphosinigrin, uric acid, midazole-4-carboxylic acid, 2-fluoro-1-methoxymethyl-ethyl ester, geranyl isovalerate, 1-nitro-ß-d-arabinofuranose, tetraacetate, glycyl-D-asparagine, α-D-xylofuranose, cyclic 1,2:3,5-bis(butylboronate), estra -1,3,5(10)-trien-17ß-ol, glucobrassicin, N-2,4-Dnp-L-arginine, dasycarpidan-1-methanol, acetate(ester) and 5alpha androstane-3,17-monooxime. The fourier transform infrared (FTIR) analysis of A. alternata proved the presence of aromatic rings, aliphatic fluoro compounds, tetiary amine, C-N stretch, ammonium ions, organic nitrate, methylene-CH. asym, and normal polymeric O-H stretch which shows major peaks at 711.73, 846.57, 873.75, 1026.13, 1149.57, 1205.51, 1238.30, 1409.96, 1631.78, 2517.10, 2854.65, 2924.09, 3059.75 and 3271.27. A. alternate had maximum zone formation (5.04 ± 0.29) mm against Klebsiella pneumonia.Keywords: Alternaria alternata, bioactive compounds, gas chromatography mass spectrometry (GCMS), fourier transform infrared (FTIR
