This study aims to knowledge the chemical composition of essential oils (EOs) extracted by hydro steam distillation of anise (Pimpinella Anisum) and fennel (Foeniculum vulgare) seeds which analyzed by gas chromatography-mass spectrometry (GC-MS). Whereas the main components of anise essential oil (AEO) were Transe Anethole (91.75%), γ-Himachalene (2.28%) and Carvone (1.71%). While the main constituents of fennel essential oil (FEO) were Estragole (74.46%), Transe Anethole (10.38%), D-limonene (10.06%) and Fenchone (3.04%). The antimicrobial activities of AEO and FEO (inhibition zone in mm) were evaluated, the results indicated that, AEO and FEO showed inhibition zones against Bacillus cereus  (8 and 8 mm), Bacillus subtilis (10 and 10 mm), Staphylococcus aureus (13 and 13 mm), Escherichia coli (12 and 8 mm), Pseudomonas aeruginosa (8 and 9 mm) and Salmonella typhimurium (10 and 9 mm), Aspergillus flavus (24 and 18 mm), Aspergillus niger (13 and 17 mm), Cladosporium sphaerospermm (14 and 14 mm), Mucor racemosus (18 and 15 mm), Penicillium chrysogenum (22 and 33 mm), Rhizopus arrhizus (26 and 24 mm), Candida albicans (18 and 28 mm), Debaryomyces hansenii (12 and 10 mm) and Pichia membranifaciens (26 and 12 mm) for AEO and FEO; respectively. It was concluded from this study that the essential oils extracted from fennel and anise show antimicrobial activity against many harmful microorganisms.