Recently, the increased consumption of mixed-grain flour products have led to improved human health in busy modern life. For this reason, the verification of commercial food authenticity is one of important subjects. The development of DNA techniques such as real-time PCR has led to the increasing efficiency of illegal food product detection. Here, we have developed a comprehensive method for detecting the grain flour of various rice cultivars in commercial food products derived from different plant species. In the genetic variation analysis of different protein coding genes on various chloroplast genomes, we found the high numbers of segregating sites in rpoB and rpoC2 more than in other genes. Thus, we have attempted to develop chloroplast DNA (cpDNA) markers, which were Os_m_rpoB in rpoB, and Os_m1_rpoC2 and Os_m2_rpoC2 in rpoC2. To assess the applicability of three cpDNA markers, we have identified the appropriate statistical measurements of each marker in various mixed-grain flour samples derived from rice cultivars and different plant species by real-time PCR, In addition, the three cpDNA markers successfully applied for detecting of nonexistent rice flour in different commercial food products.