Capillary zone electrophoresis (CZE) was used to separate cordycepin and adenosine, and determine their concentration in stroma of Cordyceps sp. These two active components of natural and cultured Cordyceps Ayushuensis were quantitatively analyzed and compared with those of cultured Cordyceps militaris. The results showed that the CZE method is a simple, rapid and sensitive method for the measurement of cordycepin and adenosine with good repeatability.