Soybean is an important worldwide crop of dietary protein and oil resources for human foods and animal feeds. However, soybean breeding and improvement has been experienced challenges by a narrow germplasms. SNP genotyping array is regarded as a promising tool for dissecting wild and cultivated germplasms to find important genes by high-density genetic mapping and genome-wide association studies (GWAS). Here, we present the establishment of a large soyaSNP 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 Axiom® SoyaSNP array. Our validation analysis for a set of 222 diverse soybean lines showed that a total of 171,161 markers were good quality for genotyping. Of the converted SNPs, 82.6% SNPs had a marker spacing of less than 9 kb and 17.4% SNPs greater than 9 kb, thereby suggesting that our array is likely suitable for GWAS of soybean germplasms. In the GWAS for seed protein content in the wild soybean germplasms with the size of 1,135 accessions, 22 loci on 12 chromosomes showed significant association (-logP>4). The highest associated peaks were shown at the 28 Mbp region on Gm05 (-logP=5.89), at 45 Mbp on Gm03 (-logP=5.32), and at 2.8 Mbp on Gm17 (-logP=5.00). Of the 22 associations, 8 corresponded with the location of previously reported seed protein QTLs and 14 regions is thought to be new QTLs for seed protein content in wild soybean. This array is being used to construct high-density genetic maps in two recombinant inbred lines and nested-association mapping populations with 30 combinations used Daepung cultivar as hub-parents, with an objective to confirm large structural variations of chromosomes using the ultra-high-density maps.