The advances in marker technologies over the last two decades and particularly in the past few years have been astounding. These advances have meant that the accuracy and speed of obtaining results has been increasing while costs have been decreasing. Among the marker types, Single Nucleotide Polymorphisms (SNPs) have not only been proven to be the most reliable and cost-effective markers available, they are also the most abundant in plants, which is why they are the most widely used for genotyping. SNPs have been used as tools for a large number of plant breeding applications including: marker assisted selection, marker assisted backcrossing, genome wide association, fingerprinting, quality control and protection of intellectual property. In cases in which little sequence data are available for a species of interest, transcriptome or genome sequencing have also proven valuable for the discovery of SNPs. In this presentation a number of practical examples will help to elucidate several of the high throughput genotyping tools available for the plant breeding community in order to make agronomically better crops for the future.