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Cerasus serrulata (Rosaceae) is an important flowering cherry resource which is valuable for developing new cultivars of flowering cherries. It is broadly distributed and possesses abundant variations. In this study, phylogeographic analysis was conducted to reveal the evolutionary history to better understand the genetic diversity and genetic structure of C. serrulata so as to provide more accurate molecular insights into better conservation and utilization of the germplasm resources. A total of 327 individuals from 18 wild populations were collected. Three chloroplast DNA (cpDNA) fragments (matK, trnD‐E, and trnS‐G) and the nuclear internal transcribed spacer (ITS) were utilized. The results showed a high genetic diversity at both species level and population level of C. serrulata. High genetic differentiation and the existence of the phylogeographic structure were detected. No significant expansion events were discovered. Two geographic lineages were inferred. One was confined to the Qinling Mountains and the Taihang Mountains. The other was from the Wuling Mountains to the Jiangnan Hilly Regions and then went northeast to the coast of Asia. In addition, some taxonomic treatments of the C. serrulata complex are discussed and reconsidered. Conservation and utilization strategies of wild C. serrulata germplasm resources were recommended. [ABSTRACT FROM AUTHOR]