Thyme (Thymus daenensis) belongs to Lamiaceae family and is one of the endemic Thymus species in Iran that grows wildly in the central and northwestern Iran and has multiple uses in food industry, sanitary, cosmetic and especially pharmaceutical. The aerial parts of Thymus species are traditionaly used as carminative, digestive and antispasmodic in the Iranian folk medicin. This plant has different compounds such as phenol, flavonoid and antioxidant activity. The aim of this study is investigation of biochemical diversity based on wild habitat altitude. For this reason 12 plants were collected from 4 region (in Nahavand) with 3 different altitude in each region (1698 up to 2248 meter above sea level). Then biologically active compounds (total phenol and flavonoid) as well as their antioxidant activity were measured. Total phenol varied from 20.19 to 26.82 (mg GAE/g dw) and the radical scavenging ranged from 89.05 to 92.72 mg/ml, as well flavonoid differ from 0.037 to .064.As a result wild habitat altitude showed significant difference in plants in the content of total phenol and antioxidant activity but there was no significant difference between plants as a matter of flavonoid.