Antrodia cinnamomea is a scarce brown-rot fungus in Taiwan. The diverse bioactive compounds with potent pharmaceutical activity make A. cinnamomea highly valuable. A. salmonea is also an important fungus growing on Cunninghamia konishii in Taiwan with several features similar to A. cinnamomea; thus, often resulted in illegal imitation of A. cinnamomea in market. In this report, we isolated the ribosome DNA (rDNA) from A. salmonea and A. cinnamomea. We were success in using the internal transcribed spacer (ITS) sequence located in rDNA to identify. Not only the sequences A. salmonea and A. cinnamomea were difference, the phylogenetic analysis confirmed that the different ITS sequence between A. salmonea and A. cinnamomea and can be a good molecular marker.