The geographical variation and domestication of tree species are an important part of the theory of forest introduction, germplasm tracing is the theoretical basis for the construction of high-quality plantations. The Chinese pine (Pinus tabuliformis Carr.) is an important native timber tree species widely distributed in northern China, but it is unclear the exact germplasm sources of the main Chinese pine plantation populations. Here, using two mtDNA markers, we analyzed 796 (873) individuals representing 38 populations of main natural and artificial populations in northern China (Shanxi, Hebei, and Liaoning provinces). The results confirmed that the core position of SX* natural populations in Chinese pine populations of northern China, genetic diversity of HB and LN plantations was higher than that of SX* natural populations, and there was a great difference in the genetic background within the groups of SX* and LN, HB showed the opposite. More importantly, we finished the “point-by-point” tracing of the HB and LN plantations task. The results suggested that almost all HB populations came from SX* (GDS*, ZTS*, GCS*, and THS*), which brought the genetic background homogeneity of HB populations. Most of the germplasm of LN plantations came from LN* (ZJS*, WF*), and the other part came from GDS* (SX*), which contributed to great differences in the genetic background within the LN group. Our findings provided a reliable theoretical basis for the scientific allocation, management, and utilization of Chinese pine populations in northern China, and for promoting the high-quality construction of Chinese pine plantations.