Pinus merkusii native Kerinci, also known as Sigi, shares the same taxonomic family as Pinus merkusii native Aceh but differs in morphology, anatomy, and physiology. Additionally, P.merkusii Kerinci has a high utilization potential but its population is decreasing and the entry of P.merkusii native Aceh around the Kerinci population can result in the erosion of the original genetic source (germplasm). The molecular characteristics of P.merkusii Kerinci and its differences with P.merkusii Aceh will be studied using rbcL. Molecular character of P.merkusii Kerinci will be compared with P.merkusii Aceh using rbcL marker in 4 individuals. The results obtained for the rbcL analysis are the percentage of conservative characters at 100%, and the four populations of P.merkusii Kerinci and Aceh are located in the same cluster and branch length. This indicates a large percentage of individual similarity between the five populations. These results tend to prove that P.merkusii Native kerinci and Aceh are located in the same taxa species and the rbcL marker cannot distinguish between Pinus merkusii native Kerinci and Aceh.