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Quince (Cydonia oblonga) is a medicinal plant and a member of family Rosaceae. It is native plant of Asia Minor and Europe. It is used in production of jam and jellies and also as a remedy of several ailments. The present study was conducted to evaluate the genetic polymorphism based on morphological and molecular traits. Different varieties of Quince were collected from different ecological zones of Khyber Pakhtunkhwa Pakistan and a total of 26 different morphological traits were recorded among studied genotypes. Based on qualitative morphological trait study, the variety collected from Tindodag was unique one with highest fruit weight (328.82 g). The lowest fruit weight (68.38 g) was recorded for Talash genotype. The Charbagh and Tindodag genotypes showed highest seed length (10.6 mm) while genotypes of Chitral was recorded as lowest (8.4 mm). Statistically, significant level of variation was noted with coefficient of variance ranged from 2.23% to 30.38%. Based on correlation analysis, fruit length had strongly correlation with fruit weight (r = 0.89**), Average Fruit width was found significant with fruit weight (r = 0.90**). Similarly, the Core Width was found strongly significant with Core Length (r = 0.95**). ANOVA analysis indicated 10 quantitative characters to be highly significant, 2 significant and 1 insignificant. Principal component analysis was also computed for the 13 quantitative traits with Eigen value of 0.48 and a total variance of 97.78%. The first principal component shows total variation of 52.52%. In PC2 the total variation was 80.15%, PC3 94.06% while in PC4 it was 97.78%. The NCBI BLAST results shows that all the genotypes have similar origin except Tindodag genotype, which shows differences in its origin. Accession number for all other genotypes is MN216014.1, while accession number of Tindodag genotype is KF861967.1. Based on this study, it can be concluded that Tindodag genotype is unique out of the studied localities. NCBI BLAST have provided further support for the drawn conclusion. [ABSTRACT FROM AUTHOR]