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In many dioecious plants, gender affects economic value, breeding schemes and opportunities for commercial harvests.Hippophae rhamnoides L. is a dioecious plant species in which female genotypes are commercially preferred over male genotypes. Its berries have rich medicinal, nutritional and pharmaceutical properties because of their large amounts of vitamins, essential oils, proteins, fatty acids, free amino acids and flavanoids. Primary limitation for breeding H. rhamnoides L. is its dioecious nature, since gender cannot be identified by traditional methods. Therefore, some reliable and quick methods need to be developed. This communication deals with the development of isozyme and RAPD markers for early sex identification in this dioecious tree. The isozyme analysis was conducted with four enzyme systems, viz. peroxidase, esterase, malate dehydrogenase and catalase. The peroxidase enzyme system produced a female specific sex marker,which successfully differentiated between the staminate and pistillate genotypes of H. rhamnoides L. Thirty five random detainer primers were used in our study and one male sex linked marker was identified.OPD-20(5-ACTTCGCCAC-3)displayed a band at 911 bp that expressed polymorphism between male and female genotypes.The staminate and pistillate genotypes could be distinguished using RAPD marker OPD-20911.These results revealed the immense potential of peroxidase isozyme patterns and RAPD as genetic markers for sex identification in H.rhamnoides L.