Soybean is a high-nutritional crop that provides a sustainable source of dietary protein and edible oil for human consumption and animal diet. In this investigation, 9 potential soybean genotypes and four commercial checks on the basis of yield and quality characters were evaluated for molecular diversity through simple sequence repeat (SSR) markers. Out of 13 gene specific SSR-loci, all markers showed association with respective trait. The heterozygosity ranged from 0.41 to 0.83, lowest to highest was observed at locus Gm012 and Gm004 respectively. Maximum gene diversity was found at locus Gm011 (0.66), while minimal was observed for locus Gm012 (0.57) with the mean value of 0.64 per marker. The polymorphic information content (PIC) was recorded highest for Gm011 (0.59) followed by Gm003, Gm006, Gm009, Satt001, while the lowest value for Gm012 (0.51). Among the 13 SSR markers, Gm011 was found to be the most informative, while Gm012 was the least insightful for the genetic diversity of studied germplasm. The polymorphic information contents (PIC) indicating a moderate level of genetic diversity exhibited by the assessed germplasm. In addition, principal coordinate analysis delineated two groups, representing two diverse gene pools in soybean collection. The UPGMA inferred three clusters based on their genetic resemblance and maturity groups. Thus, the use of substantial genetic diversity confirmed in the present study will enable soybean breeders to select diverse parents to develop high-yielding varieties with improved quality traits.