Soybean cyst nematode (SCN) is the most damaging pathogen of soybean and use of host resistance is the most effective method to manage it. Because of the multiple, complex, and ever-changing virulence phenotypes (HG types) of the pathogen in most soybean-producing regions, it is a risk to use PI 88788 as sole source of SCN resistance. Use of multiple sources of resistance or pyramiding of QTLs/genes may be an effective approach against the change of HG types. Identification of QTLs/genes and associated molecular markers for SCN resistance will be useful for soybean breeding through marker-assisted selection (MAS). A total of 272 soybean germplasm lines, collected from USDA GRIN including SCN-resistant lines with known and unknown QTLs/genes for resistance to 1 to 5 SCN HG Types (races) and SCN-susceptible lines, are being phenotyped and genotyped. SNP markers are screened and gene-based SNP markers are identified for cqSCN-001 (rhg1 and rhg1-b) on chromosome (chr) 18, cqSCN-002 (Rhg4) on chr 8, cqSCN-003 (Rhg5) on chr 16, cqSCN-005 (SCN-qtlD2) on chr 17, cqSCN-006 (SCN-qtlE) on chr 15, cqSCN-007 (SCN-qtlG2) on chr 18, SCN-qtlB1 on chr 11, and SCN-qtlO on chr 10. QTLs/genes for SCN resistance are postulated in the 272 soybean germplasm lines. Mapped positions of physical and linkage maps for the eight major QTLs/genes of SCN resistance are obtained through linear interpolation. The procedures to use QTLs/genes and implement SNP markers for SCN resistance breeding in soybean are discussed. The gene-based SNP markers will provide breeders with a tool to select SCN resistance and these germpasm lines will provide breeders with SCN resistance donors used in soybean breeding program.