Abstract: The genetic diversity and genetic relationship of 20 Morchella strains were analyzed by ISSR molecular marker method, and the microstructure of the mycelium of two Morchella strains at different growth stages in the greenhouse was analyzed by scanning electron microscopy, in dorer to provide reference for the development of Morchella germplasm resources.The results showed that a total of 35 DNA fragments were amplified by 7 ISSR primers, included 33 polymorphic bands, and the polymorphism ratio was 94.3%.When the genetic similarity coefficient was 0.74,the 20 Morchella strains were divided into 6 classes by cluster analysis.The results of scanning electron microscopy showed that the morphology of mycelium branches of Morchella Me19 and Me20 gradually changed from flat（30 days） to rounded（78 days）,and the mycelium of Me19 was more robust and dense, and grew better in the greenhouse.