Essential oils of the seed of three organically grown cultivars of fennel (Foeniculum vulgare var. azoricum, Foeniculum vulgare var. dulce, and Foeniculumvulgare var. vulgare) were examined for their chemical compositions, as well as antimicrobial and antioxidant activities. Gas chromatography/mass spectrometry analysis of the essential oils revealed the presence of eighteen major monoterpenoids in all three cultivars. However, significant differences were observed among percentages of the components. trans-Anethole (61% for azoricum), estragole (57% for vulgare), fenchone (13% for dulce), and limonene (28% for dulce) were highly abundant in all of the examined oils. Antioxidant activities of the essential oils were evaluated through DPPH radical scavenging, lipid peroxidation, and metal-chelating assays. Essential oils from the azoricum and dulce cultivars were more effective antioxidants than those from the vulgare cultivar. Antimicrobial activities of essential oils were measured against two species of fungi, two species of Gram-negative, and two species of Gram-positive bacteria. All three cultivars indicated similar antimicrobial activity. In summary, Iranian fennels have potential for use as natural antioxidants and antimicrobial agents in the industry.