To investigate the M1 biological effects of carbon ions on Lotus japonicas (MG20), dry seeds were exposed to 80MeV/nucleon carbon ions at doses of 0 Gy, 20 Gy, 50 Gy, 150 Gy, 200 Gy and 300 Gy. The dry and fresh weight, and plant height of M1 seedlings were significantly inhibited by carbon ions. The contents of chlorophyll a, total chlorophyll, and carotenoid showed the same trend with an initial increase, followed by a decrease with each dose increment; meanwhile the content of chlorophyll b showed consecutive drops. By using a random amplified polymorphic DNA (RAPD) technique, the variations of genomic DNA fingerprints of the seedlings in control and treatment groups were examined. The 2,238 bands were amplified by using 59 primers, and 400 bands showed differences, and the total percentage of polymorphism was 15.483%. The genetic similarity coefficient among the control and treatment groups were 0.710－0.863, and there were no obvious correlations between the similarity coefficients and dosages, however, differences indeed existed between the control and treatment groups. In brief, all the results showed that exposure to carbon ions had obvious biological effects on both the development and genomic DNA of the M1 seedlings of Lotus japonicus.Cited