Single nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in plants and animals. Functionally associated SNP discovery and mapping were carried out in this study using a recombinant inbred line (RIL) population of Pureunkong × Jinpumkong 2. After a total of 846 tentative consensus sequences were selected from TIGR, a total of 123 SNP markers were developed between Pureunkong and Jinpumkong 2 and 38 SNP loci were mapped in the RILs until now. By addition of these new SNP markers, 16 linkage groups (LGs) were detected with this population instead of 13 LGs with SSR markers in previous study. After developed SNP markers were mapped into the genetic map, four important soybean quantitative trait loci (QTLs), such as seed protein and oil content, number of nodules per plant and fresh nodule weight per plant, were surveyed in all LGs. Ten mapped SNP markers were located in nearby SSR markers related to seed protein content at seven LGs. Also, QTLs for number of nodules per plant and fresh nodule weight per plant were closely linked to two mapped SNP markers each. Especially, TC159475 in LG J was positioned nearby both two QTLs and Satt529, SSR marker for controlling nodule number per plant, and TC159475 were located at the same position. After SNP-based genetic linkage maps were constructed, candidate gene approach will be the next step for studying association of phenotypic traits with specific genes. Further, these will serve the plant geneticist in a number of ways from marker-assisted selection in plant improvement to map-based cloning in molecular genetic research.