Thymus capitatus is known in Palestine as ‘‘Za’tar Farsi’’ and is commonly used as tisane and was reported to possess various biological effects including antimicrobial and antioxidant activities. Although there have been many attempts to study the chemical composition (essential oil composition) of Thymus capitatus, however, to our knowledge, yet there is no extensive study available on the phytochemicals and secondary metabolites of Thymus capitatus leaves. The aim of this study was to investigate the phytochemical components in the hydro-methanolic extracts of Thymus capitatus by means of LC-MS/MS. Samples were extracted with aqueous methanol, centrifuged, followed by supernatant gathering, evaporated, and finally recovered with aqueous methanol. The analysis of the phytochemicals from M. fruticosa extract was carried out on an Agilent 1200 series LC equipped with an Agilent Zorbax C18 column. Acetonitrile and acidic water were used as mobile phases. The LC system was coupled to QTOF-MS, equipped with an electrospray ionization source operated in the negative and positive ion modes over the range from m/z 100-1100. In the present work, more than 53 phytochemical metabolites have been identified in Thymus capitatus, highlighting the importance of this plant as an important medicinal herb and as a promising source of bioactive compounds.