The pomegranate (Punica granatum L.) is an indigenous minor fruit crop of Pakistan, having a long history of cultivation as wild plant in warm temperate Himalayan range of the country; however its production is quite low to meet ever increasing market demand. Sustainable production of high quality pomegranate fruit in the world has been achieved through morpho-genetic characterization and estimation of germplasm diversity which was missing in the country. Thus it is important to estimate morphological, biochemical and genetic diversity of wild and domesticated pomegranate accessions through analysis of separate and combined data of selected wild and domesticated pomegranate accessions to be able to conserve the elite germplasm. Various levels of qualitative and quantitative morphological diversity were recorded in fruits of selected 115 pomegranate accessions. The round shape fruits were dominant in most of the commercial and wild accessions of Rawalakot whereas red color fruits and arils were predominant in wild compared to domesticated accessions. The highest value of CV was estimated in seed hardness (302.91%) followed by yellow green fruit color (215.24%), round oblong fruits (210.33%), slightly bitter arils (209.49%), pink red arils 177.33%) and white pink arils (170.97%) in all selected pomegranate accessions. The red skin color in fruit had a strong correlation (r=0.809) with red arils followed by 0.769 and 0.741% for round fruit stalked end and medium seed hardness, respectively. There was a strong positive association (0.731) of red arils with sourness and a negative correlation (-0.145) with sweetness. The wild pomegranate accessions had high CV (29.07%), for fruit weight followed by 25.61, 24.73 and 20.45% for rind weight, rind thickness and seed weight, respectively, whereas, in domesticated accessions the highest CV of 41.99% was recorded in fruit weight. Fruit weight had a strong correlation (0.79%) with rind weight and a high positive correlation was recorded between wood portion index (WPI) and aril weight in a combined analysis of wild and domesticated accessions. All domesticated accessions had a close association among fruit weight, arils and seeds, whereas the wild accessions, there was a strong association for WPI. The Abbottabad and Rawalakot accessions were highly diverse and varied not only from each other but also from accessions from other regions, whereas accessions of Muzaffargarh and Rahim Yar Khan had high similarities as shown in cluster analysis of qualitative data of all accessions. Wild and domesticated accessions successfully clustered on the basis of similarities of morphological and biochemical traits irrespective to growing regions; however, most of Muzaffargarh, Rahim Yar Khan and Mustong accessions grouped in the same class. Moreover, wild and domesticated accessions grouped in separate classes for biochemical traits while a few Chakwal, Bahawalpur and D.G. Khan accessions clustered with wild accessions for most of the morphological traits. Most of the reported SSR primers (29) in this study were efficient and showed high polymorphism with polymorphic information contents (PIC) ranging from 0.187 to 0.5598 and maximum allele frequency of xviii 0.8579% in all selected wild and domesticated pomegranate accessions. The highest genetic similarity coefficient was 30.7 to 84.76%, 21.76 to 76.78% and 21.76 to 79.88% in wild, domesticated and both wild and domesticated pomegranate accessions, respectively. The domesticated accessions clustered on the basis of genetic similarity irrespective of growing regions while wild accessions sharing common alleles were grouped in the same class based on growing regions. Thus morphological traits showed high diversity in wild accessions compared to domesticated pomegranates whereas, biochemical traits showed high diversity in domesticated accessions. In molecular studies, the SSR primers could serve as potential markers for genetic diversity estimation in Pakistani pomegranates as they proved that the genetic base of our pomegranate germplasm is broad. Molecular diversity was higher in wild accessions compared to domesticated pomegranates. These studies provide basic information for pomegranate breeding programs to develop new cultivars to broader the harvest window of high quality pomegranate fruits in Pakistan.