Through comparative sequencing of elite pepper germplasm, we have identified over 15000 SNPs in 3500 genes and determined allele frequencies for these SNPs in different types of pepper such as bell peppers and hot peppers. Using these SNP data, we are in the process of assembling an Illumina GoldenGate 1536plex assay for high-throughput SNP analysis and candidate gene studies in pepper. A set of highly polymorphic SNPs has been identified and validated in more than 100 lines and hybrids. For variety identification purposes, we also have access to several hundred microsatellite markers.