Abstract: The inter-simple sequence repeat（ISSR） molecular markers were used to explore the genetic diversity and genetic relationship of natural populations of 49 Morchella samples from 12 province regions.The aim of this study was to reveal the genetic diversity of Morchella resources, and analyze their genetic differences, so as to provide reference for the selection and breeding of Morchella resources.The results showed that the optimal ISSR-PCR reaction system was as follows 10×PCR Buffer(Mg^2-) was 2.5 μL,Mg²⁺ was 20 mmol·L^-1,DNA was 1 μg, dNTP Mix was 1 μL,Taq enzyme was 0.4 μL,primer was 1 μL,ddH₂O supplemented to 25 μL.and a total of 111 bands were amplified with 5 primers, including 110 polymorphic bands（PPB）,The proportion of PPB was 99.10%.The UPGMA method was used for cluster analysis, and 49 samples could be divided into three large groups when the number of different lines was 0.72.In conclusion, there is abundant genetic diversity among cultivated varieties of Morchella in China.