The importance of long-distance migration from low to high latitudes relative to local spread from northern refugia after the Last Glacial Maximum (LGM) remains a focus of debate for many temperate tree species. We assessed the dynamics of Chinese pine (Pinus tabulaeformis), a widespread species endemic to northern China, since the LGM by integrating cytoplasmic DNA data, mapped pollen records and ecological niche modeling. Genetic variation among 544 individuals from 50 populations spanning the entire natural species range revealed eight genetic clusters with distinct geographic distribution, indicating glacial lineages likely originating from multiple local microrefugia. Palynological evidence suggested that the northernmost part of the natural distribution originated from local postglacial spread. Niche modeling indicated high probability of the species being present in the area of the Loess Plateau and coastal areas north of the Yangtze River during the LGM. The three lines of evidence jointly suggest that the species persisted through the last glaciation in the mountains surrounding the Loess Plateau of northern China and that the current distribution of the species originated primarily from the spread of local refugial populations, instead of long-distance migration. These results cast doubt on the notion that Chinese pine migrated from areas south of the Yangtze River and underscore the importance of northern refugia.