As a novel method of mutation breeding, the low energy ion beam implantation has been widely used. The biological effects of ,Bacillus coagulans, implanted by Kaufman source and dual-Panning source have been compared. The results showed that with the same extraction voltage, the genetic stability of the third generation strain implanted by Kaufman source was 30% higher than that implanted by dual-Panning source, while the general mutation rate of the former was 2% lower than the latter. The appropriate ion source should be chosen to meet the requirement of mutation.