Bitter buckwheat, also called tartari buckwheat (F. tartaricum), contains large amount of rutin and it has antioxidant activity compared to common buckwheat. But after harvesting and processing, the discrimination of two species through visual inspection was almost impossible. Therefore we developed InDel markers to identify common and tartari buckwheat content based on the chloroplast genome sequence. We conducted complete full chloroplast genome sequence of tartari buckwheat and compared with common buckwheat chloroplast genome sequence (NC010776). Based on the mVISTA alignment, we found eight big InDel (above 50bp) regions. Among the InDel, 6 regions are intergenic region and two are genic region in ycf1. We designed InDel specific primers and applied to PCR with buckwheat genomic DNA to check the discrimination of two species. These InDel specific primers also applied to buckwheat germplasm, 75 tartari and 21 common buckwheat. Among the primers, 5 markers could be successfully amplified in all germplasm species specific amplicon. And we can detect 10pg/ul of DNA and processed food such as tea and noodle. These results could improve the QC (Quality control) of tartari buckwheat food