Background: Paeonia suffruticosa Andrew and P. lactiflora Pallas are important medicinal plants that are difficult to differentiate due to their similar appearances. The development of molecular markers will aid in the discrimination of these two species.BRMethods and Results: We found several chloroplast genomic loci that were polymorphic between P. suffruticosa and P. lactiflora. Among them, the insertion/deletion (InDel) marker PsPl-InDel-12 clearly discriminated 25 P. suffruticosa and P. lactiflora samples collected in the Republic of Korea. We were able to discriminate the two species in material of mixed status.BRConclusions: The marker developed in this study can be used to ensure P. suffruticosa and P. lactiflora quality and increase consumer confidence when purchasing medicinal products made from these species.