Abstract: In order to analyze relationship and genetic diversity among cultivars of Cerasus, 15 polymorphic primers were screened from 100 primers for genetic analysis of 208 cultivars using ISSR (inter simple sequence repeats) molecular marker technique. The results showed that a total of 91 clear bands were amplified by 15 primers, in which 83 banks were polymorphic. The average percentage of ISSR polymorphic bands was 91.21%. At the cultivar level, the percentage of polymorphic loci (PPB) was 94.03%, the Nei′s gene diversity index (H) was 0.309 5, and the Shannon′s information index (I) was 0.466 7. At the population level, the average PPB was 55.65%, H was 0.199 9, I was 0.298 0. The genetic parameters of Zhejiang population were the largest, while the Fujian were the smallest. The total gene diversity (H_t) was 0.310 7, and the gene differentiation index (G_st) was 0.356 6. The result of the Nei′s genetic distances was in agreement with that of the genetic similarity coefficients according to UPGMA (unweighted pair-group method with arithmetic means) analysis. The 208 cultivars could be divided into 2 categories. One category was cultivars from Fujian, Shandong and Yunnan Province, the other from Guizhou, Hubei, Zhejiang and Shanghai Province. The greater genetic diversity in Cerasus cultivars, and most variation was consistently originated from the interior of populations, while the cultivars distributions were obviously district specific.