The present study was carried out during 2018 and 2019 seasons . Twenty F1 and S1 progenies resulted from the combinations progenies of [Manfalouty self-pollinated, Manfalouty X Nab El-Gamal, Manfalouty open pollinated and Tahrir open pollinated ]were selected to measure several morphological quantitative and qualitative characters. Start Codon Targeted Polymorphism (SCoT) marker was used to assess the genetic. Results indicated that, MSP1 progeny gave the lowest shoot length and shoot diameter in all seasons, the same progeny gave the lowest values of number of leaves / shoot in both seasons. The MOP2 progeny is the earliest one genotype for blooming for both seasons (17 and 15 of march, respectively) in blooming. Regarding the fruit characters, TOP2 progeny gave the highest fruit diameter (99.67 and 96.00 mm), the highest fruit length (65.33 and 65.67 mm) , the fruit weight (293 and 292.3 gm) , arils weight (211 and 284 gm ) and the highest juice volume (101.7 and 84.33 ml ) in the first and second seasons, respectively. The progeny MSP2 gave the highest percent of TSS 14.93 and 15.43, in two seasons. The results of molecular analysis showed that, The ratio of polymorphism about of (48.38%), while he ratio of monomorphism about of (51.62%). UPGMA-cluster analysis discriminated the three tested cultivars and four selected progenies based on data of SCoT at 0.76 similarity. Tahrir cultivar and MOP2 progeny which produced from Open pollination of Manfalouty showed the highest value of similarity (0.96). While, TOP2 progeny showed low similarity (0.76)