Soybeans are an important ingredient in traditional foods of Japan, such as tofu, natto, miso, boiled beans, soy sauce, and edamame. Japanese soybeans have been subjected to selection for use as a food for many years and have different characteristics from those of oilseed soybeans. Useful genomic resources for studying Japanese soybeans, such as high-density linkage maps, chromosome segment substitution lines, genome sequences, high-density mutant libraries, and germplasm sets, have been developed. Because traditional foods made from Japanese soybeans are highly influenced by seed characteristics, comprehensive studies have been conducted on seed quality and composition using natural and mutant genetic resources, and several new varieties with special seed characteristics have been successfully developed. Recent advances in the genetic characterization of agriculturally important traits in Japanese soybeans, including plant type, physiological characteristics, and resistance to biotic and abiotic stresses will contribute to marker-assisted selection of new soybean varieties.