Microsatellite markers were used to identify informative markers associated with traits Sunburn sensitivity, Hull cracking sensitivity, Fruit height, Fruit diameter, Fruit shape index (Fruit height/Diameter ratio), Calyx height, Calyx diameter, Calyx height/Diameter ratio, Fruit shape, Calyx shape, Calyx type, Fruit taste, Flower height, Flower diameter, Flower height/diameter ratio and Style height. From 30 primers that were used, 7 pairs were polymorph and product 23 alleles in 202 pomegranate genotypes. The mean number of alleles were 3.28 alleles for each microsatellite locus. Polymorphic information content ranged from 0.01 (Locus MP07) to 0.56 (Locus MP39), with an average of 0.34. Stepwise regression analysis between molecular date as independent variables and morphological data as dependent variables was performed to identify informative markers associated with the studied traits. Each of the 14 traits (excluding fruit shape, calyx type, Hull cracking sensitivity and skin color) showed significant association on a total of 14 of the 23 polymorphic SSR bands. The association markers explained 2% to 29% of the variation for individual traits. The most variation of calyx height (0.29) was accounted by MP30-11, MP51-13, MP51-16 and MP07-21. SSR loci associated with fruit diameter, calyx shape and fruit size was the same. The results showed there is a significant and positive correlation among these traits. MP26 marker was linked with most traits studied in this research. Since all the used SSR loci particularly MP26 showed significant association with the studied traits, therefore, it is possible to use these markers along with morphological traits in pomegranate breeding programs for identification of suitable parents to produce mapping populations and hybrid varieties.