The State of the AJ &K- Pakistan is situated at the border of floristic regions of the world, various vicarant taxa have been differentiated and may hybridize in the same area and Pyrus is a good example. Biodiversity in indigenous Pyrus germplasm accumulated through extreme diversity in climate, geography, naturalized population and interspecific cross pollination. Further, due to silk trade route system could be promoted the phenomena of biodiversity in Pyrus species. Besides displaying high resistance to biotic and abiotic stresses, diverse germplasm are important for genetic improvement of pears. High diversity in pear species is being eroded due to the ecological damage caused by global warming and urbanization. Therefore, there is an urgent need to investigate potential and limits of molecular technique, evaluate the current genetic structure and classifying highly valuable genotypes. Genetic markers representing highest genetic diversity to all genotypes based on SSRs and Protein (SDS-PAGE) analysis showed the diversity in protein profile need to be exploited. Present study would be helpful to initiate breeding programme and to improve existing pear diverse germplasm.