SNP markers and recombination rate are critical for linkage mapping and their distribution patterns in soybean are poorly understood. The objectives of this study are to reveal the landscape of SNP distribution and recombination patterns in the soybean genome, and to map genes/QTL for traits of agronomic importance. Two recombinant inbred line (RIL) populations derived from Forrest x Williams82 (designated as FW hereafter) and Magellan x PI 438489B (designated as MPB hereafter) crosses, respectively, were used in this study. The parental lines were sequenced with Illumina sequencing technology at 10 X redundancy, and a large set of SNPs were identified. Five hundred RILs from the FW and 250 RILs from the MPB population were sequenced at low coverage (~0.15X for each RIL). Recombination breakpoints in each RIL were determined by aligning its sequences against the two parental lines, and bin maps were subsequently constructed. SNPs in different genomic regions were characterized. Fine-scale mapping of recombination rate allow us to identify recombination hot spots and cold spots. Recombination patterns and their association with different sequence features and nucleotide diversity are discussed. Some important traits are mapped with unprecedented accuracy.