Cerasus serrulata (Rosaceae) is an important flowering cherry resource. It is almost the most widely distributed species in the genus, mainly included in the subtropical and temperate China, which enables the geographic evolutionary pattern to be a representative. Besides, the morphological traits are greatly varied especially in ornamental characters. All of these makes Cerrasus serrulata a valuable research object. Thus, phylogeographic analysis was conducted to apprehend the spatial pattern and evolutionary history, which can also add insights into the phylogeography of the genus Cerasus and plants in subtropical and temperate China, as well as to deeper understand the genetic diversity and structure of the germplasm to make better and more effective utilization. A total of 327 individuals of 18 populations were collected. Three cpDNA fragments (matK, trnD-E, trnS-G) and the nuclear internal transcribed spacer (ITS) were utilized. The result showed a high genetic diversity both in species level and population level of Cerrasus serrulata. The high genetic differentiation among populations and the existence of phylogeographic structure in whole were detected. In addition, no bottleneck was identified. The the distribution pattern and center were formed before the LGM. Two geographical lineages were inferred. One was confined to Qingling Mountain and Taihang Mt. The other was from the Wuling Mt to Lu-Huang Mt, and then went northeast to the coast of Asia. Besides, taxonomic treatments of the Cerasus serrulata complex were reconsidered.