The soybean is one of the most important grain legumes, but genetic mapping had been less advanced than in other crops, which limited modern soybean molecular breeding. This chapter discusses the significant progress in mapping the soybean genome that has now been made. Also highlighted are the use of restriction fragment length polymorphism molecular markers, high-throughput genotyping markers, specific-locus amplified fragment sequencing mapping, whole-genome re-sequencing mapping and comparative genome mapping. This has allowed for the identification of quantitative trait loci or genes to improve yield, nutritional quality, as well as biotic and abiotic stress tolerances.