Background: Croton tiglium Linn., commonly known as Jayapala, in Ayurvedic pharmacopoeia, is wellknown for its purgative action. In the herbal raw drug market, seeds of Baliospermum montanum Blume., Ricinus communis Linn. and Croton roxburghii Wall. etc. are sold in the name of Jayapla seeds due to their morphological similarities. Hence their identification through molecular characters is need of the hour. Aim: Present study aims with the molecular characterization of young leaves of C. tiglium Linn. Materials & Methods: Fresh young leaves of C. tiglium Linn. were collected from its natural habitat Udupi, Karnnataka, during January 2017. It was used for molecular characterization and DNA fingerprints, by standard and most convenient Random Amplified Polymorphic DNA (RAPD) markers at Food testing laboratory, Junagadh Agriculture University, Gujarat, India. Results: All the primers gave good band patterns. Primer 5, 6, 8, 11 and 13 showed more number of light and bright bands matching characters with plant. Conclusion: Observed RAPD marker can be used to differentiate genuine as well as adulterated samples. The results may be used for the further research purposes and also required DNA Barcoding studies for further authentication.