The aim of this study was to determine of cytotoxic, antioxidant activity and phenolic profile of the two species of Thymus which are Thymus sipyleus Boiss. and Thymus leucostomus Hausskn. et Velen. (endemic). For this purpose dried herbal plant materials macerated with 70% MeOH. After evaporation and lyofilization steps the extract was analyzed with ABsciex 3200 Q trap LC-MS/MS system. Rosmarinic acid and luteolin were found as major for two species where as naringenin and apigenin glucuronide were also found as the other major compounds. The cytotoxic effects of methanolic extract of Thymus which are Thymus sipyleus Boiss. and Thymus leucostomus Hausskn. et Velen. species on the cervical (HeLa) and ovarian cancer (Skov-3) cells were investigated using colorimetric assay. The results indicated that methanolic-extract of Thymus sipyleus Boiss showed moderately active against Skov-3 cell line (IC50: 60 mu g/ml) to compared the thymus leucostomus (IC50: 360 mu g/ml). Thymus sipyleus showed no effect (IC50: 907 mu g/ml) against HeLa cell line after 72 hours. According to antioxidant activity Thymus sipyleus and Thymus leucostomus showed weak antioxidant activity with the score of DPPH IC50=0.20mg/ml and DPPH IC50= 0.13 mg/ml respectively. All the extracts showed the similar Trolox Equvalent Antioxidant activity (TEAC) with the score of 1mM TEAC. Total phenolic content of the extracts were also found as same 11mgGAE and 13 mgGAE respectively.