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Not AvailableDefinitive identification and authentication of genuine medicinal plant species is important for standardizing the herbal medicine. Ashoka [Saraca asoca (Roxb.) de Wild] a high valued medicinal plant is listed in the red data list of International Union for Conservation of Nature and Natural resources (IUCN) as ‘globally vulnerable’ species. Due to its critical status, herbal formulations and crude drugs made from S. asoca are often being adulterated with morphologically similar plant, Polyalthia longifolia. This type of substitution or adulteration adversely affects the therapeutic efficacy of the medicinal formulations. The present study was conducted to develop molecular markers for identification and differentiation of S. asoca and its widely used adulterant species P. longifolia using RAPD derived SCAR markers. Out of sixty RAPD primers used, OPQ-01 and OPQ- 06 produced specific bands of 448 and 556 bp respectively in all S. asoca lines. Similarly, OPN-19 and OPF-01 produced specific band of 535 and 336 bp respectively in all P. longifolia lines. Species specific fragments were cloned and sequenced for development of SCAR markers. Saraca specific SCAR marker SQ6-1 produced an amplicon of 193 bp from Saraca while there was no amplification in Polyalthia. Similarly, Polyalthia specific SCAR marker PN19-1 production 395 bp fragments exclusively in Polyalthia. Furthermore multiplex-PCR, using these SCAR markers, was developed for the simultaneous discrimination of both the species. SCAR markers developed could be useful for identification and discrimination of Saraca from Polyalthia or vice versa, thus finding fruitful applications in quality control for preventing adulteration in medicinal formulations of Saraca asoca.Not Availabl