Pomegranate improvement for arid regions necessitates the development of hybrids combining higher fruit yield, superior fruit quality, and clear genetic distinctness relative to locally popular cultivars. In the present study, twenty pomegranate hybrids, along with their parental lines and the control cultivar Bhagwa, were characterized using morphological, biochemical and molecular approaches. Morphological evaluation revealed that hybrid JSM-17 exhibited significantly higher fruit weight, aril weight, and juice content, with increases of approximately 28%, 53%, and 37%, respectively, over Bhagwa (p < 0.05).Yield-related traits displayed substantial variability in terms of coefficient of variation (CV) (fruits per tree= 37.19%; yield= 38.76%), with the highest yields recorded in JSM-2 (15.03 kg tree-1) and JSM-17 (13.77 kg tree-1), corresponding to 19.95% and 9.90% increases over the control cultivar Bhagwa. Biochemically, JSM-17 demonstrated superior fruit quality, characterized by higher total soluble solids (19.12 °Brix) along with significantly elevated anthocyanin content and antioxidant activity compared to other hybrids and parental genotypes (p < 0.05). The colour coordinate a*, indicative of redness in both rind and arils, showed pronounced genetic variation and attained its highest value in JSM-17. Molecular fingerprinting further confirmed the genetic distinctness of the hybrids, with JSM-17 clearly differentiated from both its parents (Jalore Seedless and Mridula) as well as the control cultivar Bhagwa. The hybrid JSM-17 was found to be promising for cultivation and further use as parent in future breeding programs aimed at enhancing pomegranate yield and fruit quality in arid conditions.