A method which uses a molecular marker technology for identifying Pleurotus citrinopileatus comprises the cultivation and collection of mycelium, the extraction of genome DNA, the establishment of the detection of a SCAR-PCR molecular marker, and the detection of a SCAR-PCR product. The method has the advantages of high sensitivity, less usage of needed DNA, and short detection time, high accuracy, easy judgment, good reproducibility, and the like, compared with conventional morphology detection, antagonistic test, and fruiting test. The method provides an effective strain identification method for the use of Pleurotus citrinopileatus germplasm resources and the registration work of new varieties.