In Korea, chilli pepper (Capsicum annum L.) is a major vegetable crop. The pepper seed market is about $35 million and the whole sale market including processed products is equivalent to $2 billion, representing the second highest market value among crops, next to rice in Korea. Since the development of elite pepper variety is so competitive, vegetable seed companies usually run two important programs to keep the credibility of seed quality. One program is to deliver F1 hybrid seeds with a high purity test to farmers. The purity control of parents and F1 hybrid to avoid any contamination is conducted by DNA markers because pepper seeds are obtained using MS line. The other program is to identify the F1 variety from other varieties by analyzing the polymorphism so that the company and/or breeder protects the intellectual property from copying by others or from non-intentional contamination. We have developed about 900 EST-SSR sets from pepper and used to both programs. A total of 66 markers were selected to identify 32 F1 varieties and their own parents. Using these markers, the purity control of F1 hybrid rose up to the highest degree. We also found several SSR markers to distinguish F1 variety from other varieties and these markers could be useful to find the uniqueness of F1 cultivar.