Peanut seeds were exposed to microwave and X-ray radiation before planting in artificially infested soil with S. rolfsii under a greenhouse and natural field conditions. Results showed a high reduction of stem rot and improvement of yield and seed oil content of peanut following seeds exposed to X-ray at 45KeV for 5 sec and MR or 30 sec compared to the control (non-irradiated seeds). Based on the RAPD-PCR mutagenic analysis of DNA peanut plants using eight ten-mer (random primers used for molecular polymorphism analysis) random oligonucleotide primers following seed irradiation, six new DNA bands, and no missing bands were detected with mutagenic frequency (20%) in plants raised from seeds exposed to MR for 30 sec. In addition, four new DNA bands were detected, and only one missing band was detected with mutagenic frequency (18.51%) in plants generated from seeds exposed to X-ray at 45 KeV for 5 sec. In contrast, the most noticeable changes were the increased number of missing DNA bands by increasing the X-ray exposure dose, where the number of missing bands was increased from 1 in 45 KeV to 3 bands in 75 KeV and 6 bands in 95 KeV. Therefore, these findings demonstrated that seed exposure to X-rays at the low dose of 45 KeV for 5 sec effectively controlled Sclerotium stem rot of peanut but caused more severe plant injuries at high radiation doses.