The genetic diversity of Xylocarpus a tree mangrove species was assessed. Three species viz., X. granatum, X. moluccensis and X. mekongensis were collected from different localities of the states of Tamil Nadu and Andhra Pradesh in India. These three species showed high degrees of phenotypic variation in the vegetative parts such as leaf, bark and root. To assess the variations at the molecular level within the three species of Xylocarpus a RAPD technique was used. A total of 283 DNA fragments were generated by 25 random primers, with an average of 11.32 easily detectable fragments per primer. A higher similarity was observed between X. mekongensis and X. moluccensis, whereas X. granatum and X. mekongensis showed lower similarity. X. granatum and X. mekongensis had a variation of more than 79 %. On the other hand, X. mekongensis and X. moluccensis seem to be closely related with 35% variation. These variations may be due to its genotypic variation, isolated distribution and adaptation to dissimilar edaphic and environmental factors. All the three species of Xylocarpus are related at various degrees. These results will be helpful in future to assess the existing interspecific genetic polymorphism in Xylocarpus species and to design strategy for their conservation.