Arnebia hispidissima, wild plant species from Boraginaceae family, accumulating Shikonin fail to produce a sufficient raw material for commercial production of Shikonin. Therefore, biotechnology can be of immense help to circumvent these problems, especially the micropropagation of plants. Additionally, Hairy Root Culture serves as an alternative approach for production of secondary metabolites in vitro. A final push is required to make this technology widely applicable for the production of pharmaceuticals, dyes and fragrances. Demands for natural products for fragrances, dyes and pharmaceuticals are increasing day by day and technology should be ready to meet the demand in coming decades. The result of present study would be very useful in increasing the yield of Shikonin and its derivatives. This is the first report on high frequency direct plant regeneration, callus induction, plant regeneration from callus cultures, efficient micropropagation, induction of Shikonin production and induction of Hairy Root Cultures through Agrobacterium rhizogenes-mediated genetic transformation studies in Arnebia hispidissima.