Artocarpus lakoocha Roxb and Pterospermum acerifolium Willd are the important anti- glycation, antioxidant and antiulcer agents in Ayurveda which is a comprehensive healthcare system. Known for its immense potential there is a need to preserve and explore their quantum of genetic variation by analysing the polymorphism between the two plants. Literature suggests that there have not been detail classification of these plants, hence we aim to analyse the interrelationship and genetic polymorphism by using RAPD markers. In this study a set of 25 plants RAPD universal primers (RPI 1- RPI-25) were used. Total Genomic DNA extracted from the leaves was used for PCR reactions. The study suggests that the genetic pattern of the two species showed the distinct variation in polymorphism at amplicons level. Each of the two plants reproduced 6 highly polymorphic bands. This approach will help in identifying genetic variation among different species and developing ways to conserve the medicinal aspects of Artocarpus lakoocha Roxb and Pterospermum acerifolium Willd. Moreover, Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Artocarpus lakoocha Roxb and Pterospermum acerifolium Willd.