The newly developed varieties, Jayoung (violet flesh color) and Hongyoung (red flesh color) that harboring various anthocyanins and flavonoids in flesh colored potato are highly increase their interesting not only for food but also functional characteristics such as anti-inflammatory effects. Up to date, most of the molecular markers developed in potato are linked to disease resistance including late blight and PVY, nematode. A few markers linked to economically important functional materials such as anthocyanin biosynthesis are published. With the low cost and high throughput of NGS (Next Generation Sequencing) technology, numerous molecular markers are highly increased in may crops. Among the molecular markers, SNPs (Single nucleotide Polymorphisms) are most useful markers owing to their large numbers in inter and intra varieties in potato. Here we reported SNPs discovery from transcriptome sequencing data acquired from colored flesh potato cultivars, Jayoung and Hongyoung with white flesh color Atlantic. Total RNA was isolated from shoot in tuber after breaking dormancy about 2cm length. Short read sequence data were obtained form Illumina Hiseq2000 and the raw dat set were trimmed with Q socore over 20. Sequencing data were align to reference genome (Solanum tuberosum v4.03, http://potatogeomics.plantbiolgy.msu.edu). About 70% of sequence read were mapped int to reference genome. 139,050, 140,976 and 146,429 total SNPs were discovered in Hongyoung, Jayoung and Atlantic, respectively. All SNPs are mapped into the psedomolecules in reference genome by chromosome. SNPs are also analyzed with homozygous and heterozygous SNPs and genic and intergenic region. SNPs are compared with Potato Infinium 8K Chip data. SNPs found in candidate genes of anthocyanin biosynthesis were discovered. These SNPs information of flesh colored potato will be further analyzed for the allele mining for anthocyanin syhthesis and control region