Ion-beam breeding technology is a method that induces mutations by causing accelerated ionized atomic nuclei to hit the genome DNA of target organisms, thereby providing a substantial amount of energy to the localized area of the genome. Here we report an improved method for the breeding of sake yeasts by ion-beam irradiation. Pre-cultivating sake yeast Kyokai no. 701（K701） in a YPDS medium containing 1M of sorbitol improved its viability on cellulose acetate membrane filters. Additionally, recovery cultivation in a YPD medium increased yeast viability to around 90 %. Similar results were confirmed with eight other Kyokai sake yeast strains. Next, K701 was irradiated with 6 different ion-beams and UV to isolate 5-fluoroorotic acid（5-FOA） resistant mutants. As a result, mutant candidates were obtained by C220, C320, He50, Ar460, and UV irradiation. None of their URA3 gene was mutated, suggesting a 5-FOA resistant phenotype for these mutants is caused by something other than uracil auxotroph. By whole genome analysis, it was found that the number of point mutation in the genome of 5-FOA resistant mutants obtained by ion-beam irradiation was fewer than those obtained by UV irradiation. It was also found that ion-beams with high liner energy transfer（LET） radiation tend to cause large-scale mutations inferred as a loss of heterozygosity（LOH）.