Rapid advances in “next-generation” DNA sequencing technology have brought the $1000 human genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped.  To capitalize on these advancements, genotyping-by-sequencing (GBS) has been developed as a rapid and robust approach for reduced-representation sequencing of multiplexed samples that combines genome-wide molecular marker discovery and genotyping.  The flexibility and low-cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding.  Applications of GBS in a range of species will be highlighted and discussed including genetic mapping, genomic selection, marker-assisted selection, characterizing genetic diversity and genome assembly.