A breeding program to improve pomegranate for desired traits should be considered. Thus, this investigation was conducted during the 2019 and 2020 seasons to study the phenotypic and genotypic characters of S1 progenies resulted from the self-pollinating Badr pomegranate cultivar. Thirteen S1 progenies were selected to evaluate their vegetative, floral and fruit characteristics. Results revealed that tree height ranged from 285 to 420 cm and trunk circumference from 31 to 56 cm. Tree no. 12 (T12) recorded the highest percentage of fruit set (24.86%) in the two seasons. The highest yield was achieved by T11 (38.00 kg) in the first season and by T7 (33.75 kg) in the second one. T12 and T7 recorded the highest fruit weight (424.27 and 348.03 g) and volume (409.00 and 427.50 cm3) across the two seasons, respectively. Soluble solids content (SSC) ranged from 9.17 to 15.40 °Brix and SSC/Acidity ratio ranged from 7.25 to 32.31. T9 and T4 showed the highest value of vitamin C (24.40 and 23.08 mg/100 ml juice), whereas T5 gave the highest concentrations of anthocyanin content (0.77 and 0.76 mg/100 ml juice), respectively, across two seasons. Total sugars ranged from 10.98 to 13.51 mg/100 ml juice. DNA fingerprinting was conducted using the SCoT marker technique. A total of eighty bands were generated from eight SCoT primers, ranging in size from 230 to 1430 bp, 57 bands (70.37%) were polymorphic, and the number of polymorphic bands varied from 2 (SCoT-01) to 13 (SCoT-04) with an average of 7.12 bands per primer. None of the used polymorphic SCoT primers could discriminate all the tested genotypes independently. The genetic similarity among the tested Badr S1 trees ranged from a maximum of 0.903 (between T4 and T6) to a minimum of 0.610 (between T2 and T5). In general, from the investigated thirteen Badr S1 progenies, six trees (T1, T3, T5, T7, T9 and T10) are promising, which showed high weight and percentage of aril, high weight and volume of fruit, high red coloration of arils, attractive red color of peel, high content of soluble solid with low acidity, high content of vitamin C and anthocyanin and good yielding. This investigation is considered a preliminary study to select new Badr S1 genotypes that could be used in further trials of breeding programs to develop new superior varieties.