Our previous studies demonstrated distant/abscopal bystander effects in A. thaliana seeds and embryos; the postembryonic development of bystander tissues, such as root hair differentiation, primary root elongation, lateral root initiation and survival, were inhibited significantly by localized irradiation with microbeam protons and low-energy ions. In the present study, we further investigated radiation-induced bystander mutagenic effects in vivo in A. thaliana plants using homologous recombination (HR) and the expression level of the HR-related AtRAD54 gene as mutagenic end points. We found that α-particle irradiation of distal primary roots of young seedlings resulted in a significant increase in the frequency of HR in the aerial plants; the increased induction of HR occurred in every true leaf over the course of rosette development. Moreover, we also found that localized α-particle irradiation of roots induced a short-term up-regulated expression of the HR-related AtRAD54 gene in the nonirradiated aerial plants. These results suggested the existence of bystander mutagenic effects in vivo in plants. Treatment with the ROS scavenger DMSO dramatically reduced the effects of localized root irradiation on the induction of HR and expression of the AtRAD54 gene in bystander tissues, suggesting that ROS play a critical role in mediating the bystander mutagenic effects in plants.