<p>Soybean is a high-nutritional legume crop providing a sustainable source of dietary protein and edible oil for human consumption and animal feed globally. In India, soybean productivity significantly lags behind the global average, largely due to its limited genetic base. Thus, understanding agro-morphological and molecular diversity among germplasm is crucial for improvement programs. In this study, 247 soybean genotypes were evaluated over two consecutive seasons (<i>kharif</i>/summer 2021–2022) for 29 agro-morphological traits using 59 simple sequence repeat (SSR) markers spanning all 20 chromosomes to assess genetic and phenotypic variations. The pooled results revealed significant variability among entries. Morphological diversity analysis (D²) grouped the genotypes into 24 distinct clusters (six polygenotypic and 18 solitary). The inter-cluster distance ranged from 5.04 to 30.26, with the highest distance between clusters 14 and 24 (30.26), followed by clusters 21 and 23 (27.97), indicating potential for selecting diverse parental lines. Principal component analysis identified five significant components accounting for 66.35% of the total variation, with plant height, seeds per pod, pods per plant, days to 50% flowering, biological yield per plant, and 100-seed weight being key traits. Out of 59 SSR loci, 21 were polymorphic, producing 69 alleles with an average of 3.290 alleles per locus. Marker Satt216 had the highest polymorphic information content (PIC) of 0.7960, with an average PIC of 0.5360; 15 markers had PIC ≥ 0.5. UPGMA clustering and neighbor-joining tree analyses of molecular data grouped the genotypes into three stratifications, confirmed by population structure analysis. The genetic diversity observed could be utilized to minimize the yield gap by developing high-yielding soybean varieties with improved traits.</p>