To study the genetic diversity of Cerasus conradinae（Koehne）T. T. Yu & C. L. Li so as to contribute to the conservation and utilization of its germplasm，the ITS sequence was amplified by PCR and then sequenced by Sanger method，and genetic analysis software was used to analyze the genetic diversity and genetic structure of 207 individuals from 10 populations of C. conradinae（Koehne）T. T. Yu & C. L. Li in Hunan province. The nucleotide diversity and haplotype diversity of C. conradinae（Koehne）T. T. Yu & C. L. Li in Hunan province was 0.00560，and 0.792 respectively. The 207 germplasms can be divided into 14 haplotypes. Among them，the population from Zhongfang County of Huaihua City has the highest genetic diversity， followed by the population from Nanyue District of Hengyang City，and the population from Suxian District of Chenzhou City had the lowest genetic diversity. The results of AMOVA analysis showed that 60% of the genetic variation existed among the populations of C. conradinae（Koehne）T. T. Yu & C. L. Li，40% existed within the populations，and there was a large genetic differentiation among most of the populations. Among them，the genetic differentiation index between populations from Suxian District and Shimen County was as high as 0.96571. The neutral test results showed that the values of Tajima′s D（1.02121）and Fu and Li′s D（1.07527） are both positive，but statistical tests were not significant（P>0.10），the results of the mismatch distribution analysis showed that the mismatch distribution presented a bimodal curve. This indicated that the population of C. conradinae（Koehne）T. T. Yu & C. L. Li in Hunan province followed a neutral evolutionary model，and might have experienced balanced selection or sudden population shrinkage during the evolution process. Mantel test showed that there was a positive correlation between geographic distance and genetic distance among the populations（r=0.3356，P=0.026<0.05）. The genetic diversity of C. conradinae（Koehne）T. T. Yu & C. L. Li germplasms in Hunan province was relatively high，and the genetic differentiations among populations were obvious and conformed to the Isolation-by-distance（IBD）model.