ORF sequence of gene Cmwc–1 and Cmwc–2, the blue light receptor, were cloned from fungus Cordyceps militaris by approach of RT–PCR. There were 1 PAS functional domains and 1 zinc finger functional domain at putative CmWC–2 amino acid sequence in Cmwc–2 ORF. The real-time PCR results showed that the translation of gene Cmwc–1 and Cmwc–2 reached their peaks in 6 h and 2 h, respectively. The relative transcription level of gene Cmwc–1 and Cmwc–2 were quite different according to their growing stages. The relative transcription level of Cmwc–1 was mainly distributed at the middle and lower section of fruiting body, and rarely spotted at the top after 50 d inoculation, while, it was mainly at the top and the middle section for Cmwc–2. There were little relative transcription level of Cmwc–1 and Cmwc–2 in abnormal fruiting body.