Six Egyptian pomegranate (Punica granatum L.) cultivars were characterized by fruit characteristics (physical and chemical) and two molecular markers; Inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP). Genetic diversity of the pomegranate genotypes was evaluated. Physical fruit traits were determined (weight, volume and diameter), calyx [diameter, length (mm) and Carpels number], fruit firmness (Newton), peel as (weight and thickness), arils weight (g), volume of juice (ml), seeds [fresh and dry weight (g)], and color parameter of (fruit skin, internal peel, arils, juice and seeds). The chemical traits such as soluble solids contents (SSC), vitamin C content, anthocyanin content, pH, and titratable acidity (TA) were assessed and wide variations were observed in each of these traits among the studied cultivars. The genetic variability and relationships among six Egyptian pomegranate cultivars were tested using ISSR and AFLP analyses. The level of polymorphism across cultivars was 53 and 90.7% as revealed by ISSR and AFLP, respectively. ISSR and AFLP revealed different genetic similarities among the six pomegranate cultivars. Each analysis differs not only in its underlying principle, but also in their in-formativeness with regard to the type and amount of polymorphism detected. Genetic similarity matrices estimated from ISSR and AFLP data, showed similarity coefficients to range from 0.77 to 0.94 and 0.33 to 0.73, respectively. ISSR and AFLP characterized the six pomegranate cultivars by a large number of unique markers being 23 and 46 unique markers, respectively. The fruit weight ranged between 479.4 to 185 g of ʻNab El Gamalʼ and ʻAssuityʼ, the firmness was 79.98 of ʻNab El Gamalʼ and 71.84 Newton of ʻManfaloutyʼ cv. The fruit peel thickness varied from 0.6 mm ʻArabyʼ, ʻHegazyʼ and ʻWardiʼ to 0.3 mm ʻAssuityʼ. The arils weight ranged from 87.5 to 275 g of ʻAssuityʼ and ʻNab El Gamalʼ cvs. The percentage net of arils weight/ fruit weight was the highest (59.34% of ʻManfaloutyʼ cv). The juice volume ranged from 62.41 to 71.81 ml/100 g arils for ʻ Wardiʼ and ʻNab El Gamalʼ cvs. The SSC content ranged between 16.01 ʻHegazyʼ and 12.55% ʻAssuityʼ. V.C. content ranged from 3.21 to 14 mg. vitamin/100 ml juice of ʻNab El Gamalʼ and ʻAssuityʼ. The anthocyanin content ranged from 1.47 to 10.03 for ʻArabyʼ and ʻHegazyʼ. The pH values varied from 3.3 (Wardi) to 2.9 (Araby). The Egyptain cultivars of pomegranate have a wide variation in the morphological and chemical characteristics for many uses of fresh fruit and of industry purpose.Keywords: Morphological and chemical fruits characterization, pomegranate, inter simple sequence repeat (ISSR), DNA markers, amplified fragment length polymorphism (AFLP)African Journal of Biotechnology, Vol. 13(2), pp. 226-237, 8 January, 201
