Molecular genetic markers represent one of the most powerful tools for the analysis of variation between plant genomes. Molecular marker technology has developed rapidly over the last decade, with the introduction of new DNA sequencing methods and the development of high-throughput genotyping methods. Single nucleotide polymorphisms (SNPs) now dominate applications in modern plant genetic analysis. The reducing cost of DNA sequencing and increasing availability of large sequence data sets permit the mining of this data for large numbers of SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies, and marker-assisted selection. Here we describe automated methods for the discovery of SNP molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Examples include SNP discovery using autoSNPdb and wheatgenome.info as well as SNP genotyping using Illumina's GoldenGate™ and Infinium™ methods.