In the present analysis Random amplified polymorphic DNA (RAPD) markers were used to assess the genetic diversity in Pterocarpus santalinus L. plant material was collected from six natural populations of Andhrapradesh, Telangana region. Six individual plants were analysed using 20 most informative RAPD primers which amplified scored DNA bands showing polymorphism. Cluster analysis UPGMA with arithmetic average formed two major clusters which illustrated that most individuals from a given population tend to cluster together and therefore 75% genetically similar than individuals from different populations. Most of the genetic variations were found to be high within population and low among populations. Similarity index revealed the close relationship of Chittoor genotype with the order of Hyderabad, Karimnagar, Khammam, Warangal and Nalgonda. Hyderabad genotype has shown more similarity followed by Karimnagar and Warangal to Nalgonda and Khammam. The maximum similarity of 89% was observed between Hyderabad and Nalgonda genotypes. Minimum similarity of 61% was recorded found between Chittoor and Warangal. The genetic diversity information reported in this study of Pterocarpus santalinus L populations is very important component for efficient conservation and effective management of its genetic resources and to obtain baseline information on its genetic diversity and population structure in order to formulate effective conservation plans.