Rice (Oryza sativa L.) is one of oldest domesticated specie and a major staple food of around 3 billion people in the world. An investigation to find out the genetic diversity among 113 cold tolerant rice accessions acquired from plant genetic resource institute (PGRI) origionally obtained from Northern Areas of Pakistan along with three check varieties (Super Basmati, IR6, and JP5) was conducted. Morpho-physiological data was recorded for 19 qualitative and 19 quantitative traits at different growth stages during the summer season 2014 at two locations. The data was analyzed by cluster analysis and principal component analyses (PCA). Results revealed significant level of variability for all the morphological traits. Maximum variation was observed in grain yield plant-1, (433.92 g) and plant height (311.28 cm). The accessions were grouped into seven clusters based on Euclidean dissimilarity index. PCA based on 19 quantitative traits showed that first five PCs accounted for 67.86% of the total variance, PCI explained 28.41%, PCII contributed 13.38% and PCIII accounted for 11.69% of total variation. Polymorphic genetic markers were also used to identify species relationship and to asses the degree of genetic diversity in the accessions. On the basis of absence and presence of 18 visible polypeptides, an electrophoretic profile was established for construction of dendrogram through UPGMA method. A significant amount of variation was revealed in Glutelin and Prolamin subunits, while low variation was observed in Albumin and Globulin subunits. It can be inferred from the present investigation that lower genetic diversity was xiv present in rice accessions based on total seed storage protein profile SDS-PAGE alone was found to be insufficient for reliable differentiation. High yielding 96 accessions were selected through morphological and biochemical characterization for the determination of allelic variability through microsatellite analysis using 36 SSR markers. An average of 3.5 alleles per locus were observed. Polymorphism Information Content (PIC) value with an average of 0.638 per locus was observed. From the results it is concluded that SSR markers were effective in detecting polymorphism in the accessions studied and other crops with high genetic similarity. Bacterial leaf blight is one of the most serious diseases of rice in world. For molecular characterization of these accessions against bacterial blight and fragrance, tightly linked STS markers were used to amplify the target fragment. Accessions were also analyzed for presence or absence of bacterial blight resistant genes (Xa4, xa5, xa13, Xa21 and fgr) through PCR amplification using STS primers. Out of 96 accessions 42 accessions were found to have Xa4 resistant gene, while 50 accessions were found to have xa13 resistant gene. Fifty two accessions were found to have xa5 resistant gene which is most prevalent gene in Northern areas germplasm, Xa21 resistance gene and fgr gene were found to be absent in the germplasm studied.