We investigated the effects of a calmodulin (CaM) inhibitor, W-7, on the expression of lignin peroxidase (LiP) and manganese peroxidase (MnP) genes in Phanerochaete chrysosporium to consider the role of cam gene, which was upregulated in parallel with the total activities of LiP and MnP in our previous transcriptomic analysis. The addition of 100 μM W-7 to the fungal cultures repressed the total activities of LiP and MnP, whereas the addition of 100 μM W-5, which is a control drug of W-7, retained approximately half of them, indicating that the effect of W-7 was attributable to CaM inhibition. Real-time reverse transcription polymerase chain reaction analysis revealed that most of lip and mnp isozyme genes predicted from whole-genome data were significantly inhibited by W-7 at the transcription level (P ≤ 0.05). These results suggest that CaM has an important role for the expression of isozyme genes of LiP and MnP at the transcription level.