Nepeta natanzensis belonging to lamiaceae family that distributed at center of Iran. The aim of this research was to phytochemical composition and estimation of antimicrobial activity essential oils from leaves, stems and seeds of Nepeta natanzensis. The essential oils were obtained by hydrodistillation and analyzed by GC and GC/MS. Our study show that α-Pinene, Limonene, α-terpinyl acetate, trans-Caryophyllne, Spathulenol, limonene, 4aα,7α,7aα- Nepetalactone, Bicyclogermacrene, Hexadecanoic acid were found as the major constituent compounds in the oils. The oils were screening to antimicrobial activity by using broth and agar microdilution methods and result show that the oils (leaf and seed) have a strong antimicrobial activity.