Although the technology of ion-beam-induced gene transfer into either plant or bacterial cells has been successfully established, relevant mechanisms have not been understood. This work aimed to study the process of induction and thus to develop applications of ion beam bioengineering. Cells of various plant tissues were bombarded in vacuum with argon and nitrogen ion beams at energies of 15-30 keV with fluences ranging from 5 × 10 14 -3 × 10 16 ions/cm 2 . The ion bombardment effects on tissue viability and neutral red dye molecule transfer into the cells through the cell envelope were investigated. The results showed that the characteristics of the tissue survival from the ion bombardment and penetration of the dye molecules into the cells through the cell envelope depended on ion species, energy and fluence. For 30-keV argon-ion bombardment at a fluence of 2 × 10 15 ions/cm 2 , the dye molecules entered the cells without fatal injury, whereas under other conditions, the dye either did not enter the cells or stained the nuclei. On the cell envelope surface, ion-bombardment-induced crater-like structures were observed. Calculations indicated that exogenous molecule transfer into living plant cells can be achieved by ion beams with appropriate physical parameters such that the ion range and the radiation damage range lie within the solid cell wall thickness.