Genetic diversity of 36 Chieh-qua Inbred lines Based on ISSR was analyzed in our research. ISSR markers were used to analyze the genetic diversity of 36 Chieh-qua inbred lines. 14 obviously polymorphic primers were selected from 100 ISSR primers for PCR amplification in 36 Chieh-qua samples. The results showed that 76 bands were amplified from 36 samples, 45 bands were polymorphic and the percentage of polymorphic bands is 59.21%. The genetic similarity coefficient of 36 Chieh-qua samples which ranged from 0.57 to 0.96 showed that genetic diversity was narrow. The cluster analysis showed that 36 Chieh-qua inbred line samples could be classified into three groups, which has a higher correlation with the geographical origin of the samples. The dendrogram could provide a scientific basis for Chieh-qua breeding and parents selection in constructing genetic linkage map of Chieh-qua.