With 15 Pleurotus eryngii Quel varieties as test materials，using ISSR molecular marker identification method，32 ISSR primers were screened from 52 ISSR primers and the DNA was amplified by PCR，the DNA sequence polymorphism was analyzed；at the same time，the varieties of mycelial growth and yield were compared.The results showed that mycelial growth rate and yield did not exhibit the characteristics of each group，the effect of mycelial growth rate and yield were more susceptible to environmental conditions and dominant or recessive gene；reference strains of genetic similarity coefficient of variation ranged 0.64-0.98.Using the UPGMA analysis showed that，in 0.87 at 15 Pleurotus eryngii Quel varieties were divided into five types.