Free radicals produced due to various environmental stresses and numerous metabolic processes ultimately lead to complete cell impairment. To combat this cellular damage organisms require dynamic defense system. In addition to inherent defense machinery, we can supplement the defense system of organisms with natural resources like herbs. The main objective of our research had been the investigation of the radical scavenging potential of folklore medicinal herb – Arnebia benthamii and its competence in protection against DNA damage. The presence of shikonin (5,8-dihydroxy-2-(1-hydroxy-4-methyl-3-pentenyl)-1,4-naphthoquinone) in the plant was confirmed by HPLC quantification from its roots. The ethyl acetate extract of 50μg/ml yields the 5.19μg/g shikonin. This ethyl acetate extract exhibited complete protection of DNA by quenching of hydroxyl radicals. The activity of plant extract was also compared with the synthetic shikonin which also validates our study that the presence of dye like substance can also be potential candidate for the augmenting antioxidant defense system.