Aim: As a highly valued fungus, Cordyceps militaris has been widely used all over the world. Although the wild resources of C. militaris are limited, the fruiting bodies of C. militaris have been successfully cultivated on a large-scale with limited Cordycepin production. However, the high-frequency degeneration of C. militaris during subculture and preservation seriously limits the development of the C. militaris industry. Methods and Results: In this study, three different techniques for strain improvement viz., protoplast fusion, UV irradiation and chemical mutagenesis were assessed for improved biomass and cordycepin production. Conclusion: It was observed that the fusant subsequently mutated were stable for many generation and yielding improved biomass and Cordycepin. It was found that fusants after mutagenesis will be genetically stable and this methodology can be used for strain improvement of genetically unstable microorganisms.