Soybean cyst nematode is the most destructive pest causing yield reduction in soybean. However, majority of resistant cultivars in the U.S. have their resistance derived from PI 88788 (rhg1) and Peking (rhg1/Rhg4). It is critical to identify new resistance genes to combat SCN. Through greenhouse evaluation of 462 accessions for SCN resistance and by using SoySNP50K data, a genome-wide association study identified 13 SNPs on five chromosomes that are significantly associated with SCN resistance. Of those, the regions on chromosomes 18 and 8 were known to be Rhg1 and Rhg4 loci. Based on this discovery, an F2:3 population derived from Lee x PI 567488B was used for genetic mapping. The result indicated that PI 567488B carries two loci for SCN resistance, which were located on chromosomes 16 and 20. The QTL identified could be used for deployment and stacking of resistance alleles to improve SCN resistance in soybean.