We analyzed the activities of specific enzymes, esterase and peroxidase, and the electrophoresis profiling of isozymes of both the second-generation (M1) and the third-generation (M2) individuals of Arabidopsis thaliana after the parental generation was treated with low-energy N+ implantation and γ-radiation. Results indicated that the mutagenic effects of both treatments were inheritable. The obvious difference between N+ implantation and γ-radial on the relationship of doses and effects was also observed. For the correlation between effects and doses, the former presented a particular saddle-like pattern, while the latter showed a pattern of linearity. Random amplification of polymorphic DNA analysis showed that the variant DNA bands were consistent in M1 and M2 generations treated with both γ-radiation and ion implantation. However, the ratio of individual plant variation between the two treatments was remarkably different.