SoybeanGDB is a comprehensive database providing informatics service to researchers focused on the genetic and genomic studies of soybean. A total of 39 high-quality soybean genomes were collected, including a Chinese soybean Glycine max [L.] Merr. cv. Zhonghuang 13. High-quality SNPs and INDELs among 2898 soybean accessions based on the genome of Zhonghuang 13 were deposited in SoybeanGDB.