This chapter reviews key developments in marker-assisted breeding of soybean. It begins by discussing types of molecular markers such as simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs). It then discusses marker assays and genotyping platforms for marker-assisted selection, including SSR marker genotyping and developments in high-throughput genotyping. The chapter then reviews applications of marker-assisted selection in soybean breeding to deal with biotic threats such as nematodes, rusts and aphids, abiotic threats such as salinity, as well as aspects of quality such as fatty acid composition. The chapter concludes by looking at developments in genomic selection.