We have used bulked segregant analysis to screen the strain-specific DNA marker associated thermophilic strain of Pleurotus eryngii. Bulked genomic DNAs of Pleurotus eryngii were amplified by randomly amplified polymorphic DNA (RAPD) using OP-A, OP-B, OP-L, OP-P, OP-R and OP-S primers to screen the strain-specific DNA marker. A unique DNA fragment of 550 bp was amplified with OP-S07 primer from the thermophilic strain and sequenced. A sequence characterized amplified region (SCAR) marker was designed on the basis of the determined sequence and named as OP-S07-1. The PCR analysis with the OP-S07-1 primer showed that this SCAR marker clearly distinguish the thermophilic strains from the control strains.