An important worldwide plant source of dietary protein and oil, modern breeding and improvement of soybean is suffered from a narrow cultivated germplasm relative to other crop species likely because of underuse of wild soybeans as breeding resources. SNP genotyping array is regarded as a promising tool for dissecting wild and cultivated germplasms to find important adaptive genes by high-density genetic mapping and genome-wide association studies (GWAS). Here, we present the establishment of a large soybean SNP array and its use for diversity analysis and high density linkage mapping. More than 4 million high-quality SNPs identified from 16 high-depth and 31 low-depth soybean genome resequencing data were used to select 180,961 SNPs for the AxiomÒ SoyaSNP array. Our validation analysis for a set of 222 diverse soybean lines showed that a total of 171,161markers were of good quality for genotyping. Of the converted SNPs, 82.6% 82.6% SNPs had a marker spacing of less than 9 kb and 17.4% SNPs greater than 9 kb with the 297 inter-SNP spacings of >100 kb and with 812 kb of the largest spacing, thereby suggesting that our array is likely suitable for GWAS of soybean germplasm. This array is being used to construct high-density genetic map in populations generated from intermatings of two cultivated and two wild soybeans, with an objective to confirm large structural variations of chromosomes using the ultra-high-density maps