The Chinese brown frog (Rana chensinensis) is a special amphibian in northern China, as it has been used widely in traditional Chinese medicine. The skin of the Chinese brown frog is also a promising resource for producing diverse antimicrobial peptides. To obtain a more comprehensive view of the metabolism and effective pharmacological components of Chinese brown frog skin, we constructed a non-normalized cDNA library from the skin. By sequencing cDNA clones at the 5′ end, we obtained 5,976 high-quality EST sequences, which clustered into 512 contigs and 1379 singletons (in all 1,891 clusters). After BLAST searches of the protein and nucleic acid databases in GenBank, we found 46.7% of clusters to have significant similarity to known sequences; 28% matched Xenopus tropicalis ESTs and 29.1% matched Xenopus laevis ESTs. Gene annotation results indicated that genes related to secretion and defensive function, such as ubiquitin, lectin, and proteinase inhibitors, are highly expressed in the skin. Whey acidic-domain proteins are also highly abundant in the skin. Furthermore, both a β-defensin and a lysozyme are transcribed in the frog skin, providing antibacterial protection. Analyses of gene ontology and KEGG metabolic pathways indicated the physiological roles of Chinese brown frog skin.