Genetic diversity between individuals can be tracked and monitored using a range of molecular markers. These markers can detect variation ranging in scale from a single base pair up to duplications and translocations of entire chromosomal regions. The genotyping of individuals allows the detection of this variation and it has been successfully applied in plant science for many years. The increasing amounts of sequence data able to be generated using next-generation sequencing (NGS) technologies have produced a vast expansion in the rate of discovery of polymorphisms, with single nucleotide polymorphisms (SNPs) predominating as the marker of choice. This increase in polymorphic marker resources through efficient discovery, coupled with the utility of SNPs, has enabled the shift to high-throughput genotyping assays and these methods are reviewed and discussed here, alongside the recent innovations allowing increased throughput.