Wild resources of <i>Auricularia cornea (A. polytricha)</i> are abundant in China, and genetic diversity and genetic relationships analysis of <i>A. cornea</i> can provide basis for germplasm resource utilization and innovation and molecular marker-assisted breeding. In this study, 22 <i>Auricularia </i>strains collected were identified as <i>A. cornea </i>based on ITS sequence analysis, and its genetic diversity was examined by ISSR and SRAP markers. The results showed that a total of 415 bands were amplified by 11 selected ISSR primers, with an average amplification of 37.73 bands per primer, and the mean values of <i>Ne, I, </i>and <i>H</i> were 1.302, 0.368, and 0.219, respectively. A total of 450 bands were amplified by 10 SRAP primers, with an average of 45 bands per primer, and the average of <i>Ne, I,</i> and <i>H</i> were 1.263, 0.302, and 0.183, respectively. The unweighted pair-group method with arithmetic means analysis based on ISSR-SRAP marker data revealed that the genetic similarity coefficient between the tested strains was 0.73-0.97, and the strains could be divided into five groups at 0.742, which had a certain correlation with regional distribution. The results of PCOA and population structure analysis based on ISSR-SRAP data also produced similar results. These results demonstrate the genetic diversity and distinctness among wild <i>A. cornea</i> and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of <i>A. cornea </i>resources.