Antrodia cinnamomea is reinstated as the correct name for a basidiomycete consistently associated with Cinnamomum kanehirai. Antrodia salmonea nov. sp., causing a brown heart rot of Cunninghamia konishii in Taiwan, is described and illustrated. Antrodia cinnamomea and A. salmonea are morphologically similar but can be separated by pore surface color of basidiomata and host preferences. Moreover, pairings between monokaryons of A. cinnamomea and those of A. salmonea demonstrate that these two fungi have different mating systems.