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To obtain a higher cordycepin production using Cordyceps militaris mutant obtained by a new mutagenesis technique called ‘ion beam’.Successful irradiation of C. militaris NBRC 9787 by a proton beam with high energy was performed, and 30 classes of 8-azaadenine-and 28 classes of 8-azaaguanine-resistant mutants were obtained on mutant screening, of which seven classes were selected as promising preliminary mutants having an antibacterial ability as an index of cordycepin production. In a surface liquid culture technique, some of the 8-azaadenine-resistant mutants gave a better performance for the cordycepin productivity; in contrast, among the 8-azaaguanine-resistant mutants, it was shown that mutant no. G81-3 was much better than the control in the metabolic rate of glucose and the cordycepin productivity. In primary optimization using the enriched medium, the cordycepin production was 3·1 and 1·8 g l−1 on 21-day culture for mutant no. G81-3 and the control, respectively. The cordycepin production obtained by the mutant was 72% more than the control.The mutant obtained by proton beam irradiation had higher productivity of cordycepin than that of the control.The mutant obtained by irradiation had a superior production performance of cordycepin, and therefore, it could be used in the realm of applied industrial biotechnology for the large-scale production of cordycepin.