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The study of population genetic structure and historical dynamics of species with disjunct distribution can reveal the mechanisms through with they were formed. <i>Pinus densiflora</i> is an essential tree species with ecological and economic value, and its natural distribution shows a disjunct pattern. Using transcriptome-level SNP data from 220 samples representing 32 naturally-distributed populations in East Asia, we investigated <i>Pinus densiflora</i> genetic diversity and structure, divergence time, and ancestral distribution. We identified five subpopulations which diverged approximately 2.02–1.49 million years ago, and found relatively low genetic differentiation among the three large subpopulations (SL, JH, and JK). Northeast China is the most likely origin, and its current distribution is the result of dispersal and vicariance events. It migrated southwest through the Liaodong Peninsula to the Shandong Peninsula and southeast through the Korean Peninsula to Japan. These results provide a basis for the conservation and management of <i>P. densiflora</i> in the future and the evolutionary study of species with similar life histories.