Cordyceps sinensis (CS) is well known as an ancient Chinese herb. It is used to expand bronchial smooth muscles, inhibit tumor growth and decrease blood pressure. Cordyceps sinensis is composed of two parts. One is the dead larvae body; the other is the stroma like withered grass. Up to now, few genome database articles about Cordyceps sinensis have been reported. In this study, two cDNA libraries were constructed using the worm part and grass part respectively for the first time. 12192 and 15456 clones from the worm-part (CSCA) and grass-part (CSBA) library were respectively picked. Sequences derived from CSCA were clustered into 1333 contigs and 2469 singlets, while those from CSBA were clustered into 1297 contigs and 2875 singlets. These ESTs include sequences representing a significant portion of proteins encoding genes in cell signalling, metabolism, information storage and processing. Some enzymes encoding genes were also found and linked with CS’s physiology such as proteases, peptidases, lipases and chitinase. Pairwise comparison between the two cDNA libraries was also studied. Some ESTs were found only in CSCA and some only in CSBA. Finally, a comparative genomics research was performed with Fusarium graminearum, Aspergillus nidulans, Neurospora crassa and Saccharomyces bayanus. The results indicate that the fungus’ genes maybe have complicated variation at the nucleic acid level, but the proteins translated are still conservative. Cordyceps sinensis (CS) is well known as an ancient Chinese herb. It is used to expand bronchial smooth muscles, inhibit tumor growth and decrease blood pressure. One is the dead larvae body; the other is the Up to now, few genome database articles about Cordyceps sinensis have been reported. In this study, two cDNA libraries were constructed using the worm part and grass part for the first time. 12192 and 15456 clones from the worm- (CSCA) and grass-part (CSBA) library were respectively picked. Sequences derived from CSCA were clustered into 1333 contigs and 2469 singlets, while those from CSBA were clustered into 1297 contigs and 2875 singlets. These ESTs include sequences represent a significant portion of proteins encoding genes in cell signaling, metabolism, information storage and processing. Some enzymes encoding genes were also found and linked with CS’s physiology such as proteases, Some of the ESTs were found only in CSCA and some only in CSBA. Finally, a comparative genomics research was performed with Fusarium graminearum, Aspergillus nidulans, Neurospora crassa and Saccharomyces bayanus The results indicate that the fungus’ genes maybe have complicated variation at the nucleic acid level, but the proteins translated are still conservative.