Peanut is a major crop in Taiwan and it has high oil and protein content, which provide high nutritional values. The production area is around twenty thousand hectares. Taiwan has officially applied for joining the Comprehensive and Progressive Agreement for Trans-Pacific Partnership and more frequent international agriculture interactions are expected in the future. Variety identification technique plays an important role in protecting consumer rights and breeder intellectual property rights. The traditional identification technique is based on phenotyping and its application is limited by environment. The current genotyping technique is suffered from poor repeatability and low polymorphism. In this study, single-nucleotide polymorphism (SNP) was performed. There were breeder seeds of 12 commercial varieties were collected for conducting experiments. Breeder seeds were planted in Taiwan Agricultural Research institute for two seasons (fall season in 2017 and spring season in 2018). There were 26 SNP markers utilized to discriminate 12 varieties. The purity on each SNP location of each variety was estimated. The variation rates of each variety were also calculated. The minimum number of a marker set for identification was ten, which can efficiently differentiate 12 varieties. It is a very useful toolkit for variety identification and can be expanded and updated in the future when the new cultivar is released.