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A reliable, qualitative PCR-based detection method for the traceability and authentication of common and Tartary buckwheat was developed. Five InDel markers developed from chloroplast genome variation between the two species were applied for 96 buckwheat accessions and all accessions were easily differentiated as Tartary and common buckwheat using these markers. We also determined the sample detection limit by PCR and qPCR as 0.001 and 0.02 ng/µl, respectively. InDel markers could detect the mixture of two species flour up to 10% contamination. InDel markers were also applied to processed foods such as noodles and tea, and we found that species-specific PCR bands could be used to identify buckwheat even after processing. Hence, these InDel markers are simple with higher specificity and sensitivity and are reliable for the authentication of buckwheat processed foods.

Application of InDel markers based on the chloroplast genome sequences for authentication and traceability of tartary and common buckwheat