A total of 2,765 accessions were used as the initial set having both seed coat color and 100-seed weight data. As a result of molecular profiling using six SSR markers followed by stratification based on their usages, 335 accessions(12.1%) were selected by clustering based on UPGMA. Since 75 out of 335 accessions were mixed in phenotypic traits as a result of characterization, 260 accessions were finally set as a core set. This core set revealed nearly the same diversity compared with the other results on morphological traits of Korean soybean landraces. In total, 115 alleles(19.2 alleles per locus) were detected in the initial set and 79 alleles(13.2 alleles per locus) were detected in the core set. All 30 major alleles were present in the initial set and in the core set as well. In allele coverage, the core set was 71.4% of the initial set. These comparisons of number of alleles, gene diversity and coverage indicated that the core set represented the entire set well.