Medicinal plants are potential sources of natural compounds with biological activities and therefore attract the attention of researchers worldwide. The objective of this research was to determine the chemical composition of methanolic flowers extract. The phytochemical compound screened by GC-MS method. Forty nine bioactive phytochemical compounds were identified in the methanolic extract of Artemisia annua. The identification of phytochemical compounds is based on the peak area, retention time molecular weight, molecular formula, MS Fragment-ions and pharmacological actions. GC-MS analysis of Artemisia annua revealed the existence of the 1,2-15,16-Diepoxyhexadecane, 1-Methylcycloheptanol, 3,5-Hexadien-2-ol2-methyl, Cholestan-3-ol,2-methylene, (3?,5?), 2,5-Octadecadiynoic acid, methyl ester, Cyclohexene,1-methyl-5-(1-methylethenyl), Cyclohexene,4-isopropenyl-1-methoxymethoxymethyl, Exo-2,7,7-trimethylbicyclo[2.2.1]heptan-2-ol, 2(3H)-Furanone,5-ethenyldihydro-5-methyl, 2H-Benzo[f]oxireno[2,3-E]benzofuran-8(9H)-one,9[[[2-(dimethylamin), 2-Furanmethanol,5-ethenyltetrahydro-?,?,5-trimethyl-,cis-, 5,8-Decadien-2-one,5,9-dimethyl-,(E)-, Methyl 6-oxoheptanoate, Dodecanoic acid,3-hydroxy-, Isophorone, 2H-Benzo[f]oxireno[2,3-E]benzofuran-8(9H)-one,9-[[[2-(dimethylamin), 2(3H)-Benzofuranone, hexahydro-7a-methyl-, 10-Undecen-1-al,2-methyl-, 1,4-Methanoazulen-7-ol,decahydro-1,5,5,8a-tetramethyl-,[1s-(1?,3a), 3,5-Heptadienal,2-ethylidene-6-methyl-, 1,6-Dimethylhepta-1,3,5-triene, 1(2H)-Naphthalenone,octahydro-4-hydroxy-,trans, Trans-Z-a-Bisabolene epoxide, 7-epi-cis-sesquisabinene hydrate, Geranyl vinyl ether, Cyclohexanone,2,2-dimethyl-5-(3-methyloxiranyl)-,[2?(R*),3?]-(.+-.)-, Spiro[4.5]decan-7-one,1,8-dimethyl-8,9-epoxy-4-isopropyl-, 6-epi-shyobunol, 3,6-Diazahomoadamantan-9-one Hydrazone, Cholestan-3-ol,2-methylene-,(3?,5?)-, Ingol 12-acetate, Geranyl isovalerate, 1-Ethynyl-3,trans(1,1-dimethylethyl)-4,cis-methoxycyclohexan-1-ol, 1b,4a-Epoxy-2H-cyclopenta [3,4]cyclopropa[8,9]cycloundec[1,2-b]o, I-(+)-Ascorbic acid 2,6-dihexadecanoate, 9,12,15-Octadecatrinoic acid, 2,3-dihydroxypropyl ester, (Z,Z,Z)-, 1-Heptatriacotanol, Propanoic acid, 2-[5-(2-hydroxypropyl)tetrahydrofuran-2-yl]-,1-[5-(1-m), 10,13-Dioxatricyclo[7.3.1.0(4,9)]tridecan-5-ol-2carboxylic acid, 9-Octadecenamide,(Z)-, Lupeol, 9-Desoxo-9-x-acetoxy-3,8,12-tri-O-acetylingol, Olean-12-ene3,15,16,21,22,28,-hexol,(3?,15?,16?,21?,22?)-, 2,4,6-Decatrienoic acid, 1a,2,5,5a,6,9,10,10a-octahydro-5,5a-dihydro, Pregn-5-en-20-one,3,8,11,12,14,-pentahydroxy-,(3?,11?,12?,14?)-, Spirost-8-en-11-one,3-hydroxy-, (3?,5?,14?,20?,22?,25R-,(+)-y-Tocopherol,O-methyl-and 1-Phenanthrenecarboxylic acid, tetradecahydro-7-(2-methoxy-2-oxoe. The FTIR analysis of Artemisia annua flowers proved the presence of alkenes, aliphatic fluoro compounds, alcohols, ethers, carboxlic acids, esters, nitro compounds, alkanes, H-bonded H-X group, hydrogen bonded alcohols and phenols. Methanolic extract of bioactive compounds of Artemisia annua was assayed for in vitro antibacterial activity against Escherichia coli, Pseudomonas aerogenosa, Proteus mirabilis, Staphylococcus aureus and Klebsiella pneumonia by using the diffusion method in agar. The diameters of inhibition zones ranged from 5.01±0.200 to 0.700±0.106 mm for all treatments.