Cordycepin is one of the effective contents in Cordyceps Sinensis . This paper adopted HPLC technique to determine the Cordycepin in \%Cordyceps Barnessii\% Thwaites and \%Cordyceps Sinensis\%.The result is that the Cordycepin of \%Cordyceps Barnessii\% Thwaites (392 mg/100g) is higher than the Cordycepin of \%Cordyceps Sinensis\% (332 mg/100g).The medical use of \%Cordyceps Barnessii\% Thwaite in this respect is better than \%Cordyceps Sinensis\%.