In order to address the limitations of existing genotyping technologies, we have developed random Sequenced-based Genotyping (rSBG). rSBG incorporates the high-throughput sequencing capacity of the Illumina® HiSeq™ sequencer and the genome complexity reduction capabilities of AFLP®, to score random markers across an entire genome. Depending upon the needs of the user, this method allows for fine-tuning of both the optimal number of samples to be pooled, as well as the desired number of SNPs. Additionally, rSBG analysis pipelines have been developed for processing the vast amounts of data and subsequent mining of the SNPs and genotypes. Using rSBG, genome-wide SNP discovery and genotyping of large populations can be achieved in one single experiment. Applications of rSBG in various crops will be presented. Through these examples, we demonstrate that rSBG technology is an efficient and highly robust sequence-based genotyping method. The AFLP® and rSBG technologies are covered by patents and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. Other brand names and/or trade names may be (registered) trademarks of their respective owners.