Ionizing radiation directly and indirectly affects gene expression within the plant genome. To access the physiological response of rice to different types of ionizing radiation, rice seeds were exposed to gamma-ray and ion beam radiation. Exposure to ionizing radiation dramatically decreased the shoot length compared with non-irradiated plants. Fluorescence-activated-cell-sorting (FACs) was used to measure DNA contents. There were significant correlations of dose-dependent between irradiated plant and non-irradiated plant. The radicals induced by the ionizing radiation in the plant could be observed by electron spin resonance (ESR). It was confirmed that the number of free radicals in cell was greatly increased all irradiated plants than non-irradiated plant. A significant positive correlation was shown between ionizing radiation dose and signal intensity. In order to determine the Genetic diversity, AFLP analysis was conducted with the irradiated plant and non-irradiated plant. Based on band patterns, the cluster analysis was conducted to evaluate the genetic variation by using the UPGMA (Unweighted Pair Grouping Method of Averages). Genetic diversity of irradiated plants by low dose ion beam was the closest non-irradiated plant and irradiated by high dose gamma-ray was the furthest from non-irradiated. We describe the detailed methods of ionizing irradiation and discuss its applications in genetic research as well as plant breeding.