In this study, 47 landraces, 16 genotypes from NARC collection and 18 ancestral lines of US germplasm, in total 81 Soybean [Glycine max (L.) Men] genotypes were assessed, to molecular and morphological characterization. The genetic diversity was evaluated with 20 Random Amplified Polymorphic DNA (RAPD) markers and 7 morphological characters. Chi-square test for homogeneity showed significant variability for all investigated characters. Only six RAPD primers were polymorphic that showed polymorphism in 29 out of 81 genotypes. The remaining primers were excluded from the molecular study. Pair-wise dissimilarity matrix for each primer followed by an average was calculated using bivariate data set generated from all loci of the primers. A total of 474 loci were detected with an average of 79 loci for each primer and 16.32 loci were amplified genotype. Cluster analysis showed that genetic diversity exists among all three groups (land races, collection from NARC and US ancestral). High level of genetic polymorphism was observed based on the six RAPD markers. A dendrogram was constructed using Unweighted Pair Groups of Arithmetic Means, which distinguished the genotypes into four major groups. Group-IA comprised eleven land races, two US genotypes and four NARC genotypes. Group IB comprised of eight US genotypes. Group-IIA comprised of one US genotypes and one land races genotype. Group-IIB comprised of one US genotype and one NARC genotype. Based on molecular study soybean genotypes code 8-7 (land races) and U14 (US genotype; Ralsoy) showed maximum genetic distance. This information can be utilized for genetic analysis, genotype identification from different sources and development of improved germplasm.