This study was conducted to distinguish the pines that are too similar to differentiate using conventional methods. Pinus densiflora and Pinus sylvestris have similar anatomical structure. They both have window-like pits and dentate ray tracheids, so it is not easy to distinguish the plants. We tried to find molecular markers by comparing chloroplast DNA sequences to differentiate the pines growing in Korea. We used P. densiflora, P. densiflora for. multicaulis, P. sylvestris, P. rigida, P. rigitaeda, P. koraiensis, and P. bungeana for this study. We found that the non-coding intergenic region of trnT(UGU) and trnL(UAA) genes have differences among the species. We designed a primer set to amplify the region efficiently and compared the PCR product sequences using CLC Workbench programs to find the polymorphism. We could distinguish the species using the sequences of the amplified region and the sequences were reproducible from the pines collected in Korea.