Genetic variation in wild soybean (Glycine soja Sieb. and Zucc.) is a valuable resource for crop improvement efforts. Soybean is believed to have originated from China, Korea, and Japan, but little is known about the diversity or evolution of Korean wild soybean. Therefore, in this study, we evaluated the genetic diversity and population structure of 733 G. soja accessions collected in Korea using 21 simple sequence repeat (SSR) markers. The SSR loci produced 539 alleles (25.7 per locus) with a mean genetic diversity of 0.882 in these accessions. Rare alleles, those with a frequency of less than 5%, represented 75% of the total number. This collection was divided into two populations based on the principal coordinate analysis. Accessions from population 1 were distributed throughout the country, whereas most of the accessions from population 2 were distributed on the western side of the Taebaek and Sobaek mountains. The Korean G. soja collection evaluated in this study should provide useful background information for allele mining approach and breeding programmes to introgress alleles into the cultivated soybean (G. max (L). Merr.) from wild soybean.