Achillea fragrantissima Sch. Bip. (Asteraceae) has been reputed in folk medicine of the Arabia region and Egypt for the treatment of many diseases. Air dried aerial parts of A. fragrantissima were extracted with 70% aqueous ethanol and fractionated with petroleum ether, dichloromethane, n-butanol and ethyl acetate fractions. Among them, dichloromethane showed the highest activity and was subjected to separation and purification by various chromatographic techniques. Five flavones and one phenolic acid were isolated and identified as acerosin (1), cirsimaritin (2), cirsiliol (3), luteolin (4), apigenin (5) and caffeic acid (6), respectively. Acerosin, the flavone of higher concentration isolated for the first time in genus Achillea, showed promising cytotoxic and radical scavenging activity. Molecular modeling of acerosin indicated its ability to bind in a co-crystallized ligand-like manner with kinase enzyme (FAK), namely with Cys502, alongside extra binding interactions with Glu430, Lys454 and Asp564. Total protein profiling of A. fragrantissima DNA was performed using polyacrylamide gel electrophoresis (PAGE) for characterization of plant where the total number of bands recovered was 4.