The recent amendment of the Plant Variety Protection Law in Japan has extended plant breeders’ rights to cover the harvested materials and manufactured products from a cultivar. The Government Quality Labeling Standards require proper food labeling, which includes cultivar names if they appear on the product label. To protect the breeder’s right and ensure the proper labeling of wheat products, we have developed simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs) to identify the wheat cultivars used in wheat products. From a total of 3,759 SSR sites found in the EST data base, PCR amplification was tested at 186 sites in 14 wheat cultivars. We also confirmed that the markers did not occur in other crops, and so can accurately identify wheat cultivars used in products blended with these crops. A total of 10 SSR sites were finally selected and their capacity to identify 41 Japanese cultivars and 17 USA, Australian, or Canadian cultivars was examined. These SSR markers are sufficient to distinguish the Japanese cultivars from foreign cultivars and to individually identify the major Japanese cultivars, such as Hokushin and Norin 61. The SSR markers can also determine the wheat cultivars used in processed foods.