The genetic diversity of 16 Paeonia rockii lines in one population was analyzed by using inter-simple sequence repeat markers (ISSR).Fifteen primers selected from 100 primers were used for ISSR amplification.A total of 134 bands were generated,of which 96 bands were polymorphic bands (the percentage of polymorphic band,PPB=71.6%).According to the results of ISSR amplification,which were analyzed to Jaccard similarity coefficient by NTSYSpc 2.10e software,the genetic similarity coefficient varied from 0.45 to 0.93.The clustering dendrogram was constructed by UPGMA method.Sixteen P.rockii materials were divided into four major groups while the similarity coefficient was 0.534.Class Ⅰ included six of P.rockii materials,and five in six was crown form,left a single form species.But other classes also have crown flower varieties.Class Ⅱ had an anemone form species,it was the only anemone species elected in the selected materials.Four different color and form materials were clustered into Class Ⅲ,suggest that the character of closer phylogenetic relationship species were varieties.A group of Class Ⅳ included four white flowers materials,whose form were different.Group B was P.rockii ‘Yinxiannv’ alone ,it was the only red material selected.Thus,genetic clustering classification of different resemble coefficients was not consisted with that based on the flower color and form.