Aims: Isolation, characterization and identification of Phaffia sp. ZJB 00010, and improvement of astaxanthin production with low-energy ion beam implantation. Methods and Results: A strain of ZJB 00010, capable of producing astaxanthin, was isolated and identified as Phaffia rhodozyma, based on its physiological and biochemical characteristics as well as its internal transcribed spacer (ITS) rDNA gene sequence analysis. With low-energy ion beam implantation, this wild-type strain was bred for improving the yield of astaxanthin. After ion beam implantation, the best mutant, E5042, was obtained. The production of astaxanthin in E5042 was 2512 mu g g(-1) (dry cell weight, DCW), while the wild-type strain was about 1114 mu g g(-1) (DCW), an increase of 125.5%. Moreover, the fermentation conditions of mutant E5042 for producing astaxanthin were optimized. The astaxanthin production under the optimized conditions was upscaled and studied in a 50-l fermentor. Conclusions: A genetically stable mutant strain with high yield of astaxanthin was obtained using low-energy ion beam implantation. This mutant may be a suitable candidate for the industrial-scale production of astaxanthin. Significance and Impact of the Study: Astaxanthin production in Phaffia rhodozyma could be fficiently improved by low-energy ion beam implantation, which is a new technology in the mutant breeding of micro-organisms. The mutant obtained in this work could potentially be utilized in industrial production of astaxanthin.