Jamun (Syzygium cumini Skeels) is a nutritionally dense fruit recognized for its antioxidant activity, total phenols, anthocyanins, and vitamin C. These attributes not only enhance its value as a fresh fruit but also make it an essential raw material for food, pharmaceutical, and cosmetic industries. Despite its potential, the systematic improvement of jamun has been limited. This study evaluated the genetic diversity of 23 genotypes through morphological, biochemical, and SSR molecular characterizations to identify promising lines for breeding and industrial use. The evaluation was conducted from 2023 to 2025 at ICAR-IIHR, Bengaluru, and IIHR-CHES, Hirehalli, India. Morphological characterizations were conducted according to DUS guidelines, while biochemical profiling included total soluble solids (TSS), titratable acidity, vitamin C, total phenols, anthocyanins, and antioxidant activity. Multivariate analysis was used for clustering. Molecular diversity was assessed using 50 SSR markers. Substantial variability was recorded for fruit traits (weight: 1.97–18.32 g, pulp: 66.50–92.26%, and TSS: 10–18.2 °Brix). Biochemical diversity included titratable acidity (0.43–2.67%), vitamin C (23.40–65.07 mg/100 g), total phenols (120.78–936.26 mg GAE/100 g), antioxidant activity (307.78– 2493.91 mg AEAC/100 g), and anthocyanins (42.59–268.50 mg/100 g). Multivariate analysis grouped the genotypes into three clusters, with CHESHJ-XI/3, CHESHJ-V/1, and CHESHJ-Wd-1 exhibiting the highest nutraceutical richness. SSR analysis revealed high polymorphism (mean PIC = 0.687), with CHESHJ-Wd-1 being the most divergent genotype. The identified diversity emphasizes jamun’s potential as a functional food and industrial resource. Genotypes Kaithnal and AJG-85 were superior for fresh fruit quality, CHESHJ-XI/3 and CHESHJ-V/1 for nutraceutical traits, CHESHJ-Wd-1 for antioxidant potential, and CHESHJ-Wt-1 for dwarf stature with high TSS. These findings support targeted breeding, conservation, and value addition, reinforcing the significance of jamun in food security and nutraceutical innovation.
