Nowadays, the overdose use of antibiotics and the increase of microbial resistances have made researchers to carry out more studies about the new drugs with new chemical composition. In order to produce these new drugs, different species of special plants can be useful by scientists and researchers. Base on this, the leaves and fruits of Juniperus excelsa and Juniperus horizontalis were collected from Iranian National Botanic Garden. Essential oils were isolated by hydro-distillation method. The essential oil components were analyzed by gas chromatography-mass spectrometry (GC-MS). The yields of the leaves and fruits of J. excelsa and J. horizontalis essential oils were 0/79 to 4/15% and 1/083 to 2/7%, respectively. There were 15 and 27 components in the essential oil of J. excelsa and J. horizontalis, respectively. The major compound in the essential oils obtained from the leaves and fruits of J. excelsa were α-pinene (79/95 and 89/49%, respectively). The main compound in the essential oils obtained from the leaves and fruits of J. horizontalis were sabinene (30/21 and 38%, respectively). In addition, bornyl acetate (10/66%) and delta-cadinene (3/79%) were identified as major components in the essential oil of the leaves obtained from J. horizontalis. Juniper essential oils were evaluated for the antibacterial activity against thirteen bacterial species by disk diffusion and micro dilution method. Juniper essential oils showed more antibacterial activities against Gram-positive as compared to Gram-negative bacteria species. The antibacterial activity of essential oils may be related to presence of α-pinene, limonene, and sabinene which are known to have antibacterial properties.