Copper-tolerant brown-rot fungi are able to degrade wood treated with copper or copper-based wood preservatives. This research used quantitative reverse transcriptase polymerase chain reaction to explore what genes of the brown-rot fungus, Fibroporia radiculosa, were expressed when the fungus was overcoming the wood preservatives and decaying the wood. Aryl alcohol oxidase, catalase, oxalate decarboxylase 2, and copper resistance P-type ATPase pump had higher expression on alkaline copper quat type D treated wood compared with week 1. In addition, two genes had high expression at week 5; glycoside hydrolase 5 and glycoside hydrolase 10 when wood strength loss was around 50%. Glyoxylate dehydrogenase had high expression until week 8. This gene might be involved in the production of oxalate. Laccase, oxalate decarboxylase 1 and isocitrate lyase were not differentially expressed, suggesting that these genes were not involved in the decay process of alkaline copper quat-treated wood. These results are important to understand the genes that are involved in the mechanism of copper tolerance and wood decay in F. radiculosa.