The forward and reverse cDNA subtractive libraries before and after the toxic effect of alpha-amanitin were constructed by suppression subtractive hybridization and randomly selected clones from each subtractive library were screened by PCR and dot blot hybridization. A total of 85 genes with altered expression were finally identified, with 41 genes from the forward library and 44 from the reverse library. Subsequently, the antagonistic effects of candidate traditional Chinese medicines were evaluated based on the genetic transcription levels of the genes with significant altered expression, including Catnbeta, Flt3-L, IL-7r and Rpo2-4. The results indicated that Silybum marianum (L.) Gaert and Ganoderma lucidum had significant down-regulated effects on the transcription level of Catnbeta that was up-regulated by alpha-amanitin, and the two herbs also up-regulated the transcription levels of Flt3-L and Rpo2-4. Silybum marianum (L.) had significant up-regulated effects on the IL-7r that was down-regulated by alpha-amanitin. These preliminary studies suggested that Silybum marianum (L.) and Ganoderma lucidum were effective antagonists against the toxicity of alpha-amanitin.