This study was designed for the purpose of establishing an effective way for rapid identification of Lentinula edodes strains based on DNA molecular marker. The RAPD (Random Amplified Polymorphic DNA) analysis was conducted on 14 cultivated strains of Lentinula edodes. A specific RAPD marker with a length of 1166kb, XG1166, could be generated from the Lentinula edodes strain 162. Subsequently, the RAPD marker was converted into more stable SCAR(Sequence Characterized Amplified Region) marker by the use of molecular cloning technology. In the same way, another SCAR marker with a length of 347kb, SX347, was obtained from Lentinula edodes strain Shenxiang-10. The results showed SCAR marker of strain 162 or Shenxiang-10 acquired based on this study could be used as a specific DNA fingerprint to identify strain 162 or Shenxiang-10 whithin one day. Consequently, it was suggested that SCAR molecular marker technology is an effective new way to identify Lentinula edodes strains more accurately and rapidly and it could be applied widely in the protection of germplasm resources, classification and identification distinguishing false strains of edible mushroom.