The plant hormone abscisic acid (ABA) plays a central role in adaptive stress responses to abiotic environments, but little information exists about its responses to implantation with low-energy ion beams. The genes related to ABA synthesis including zeaxanthin epoxidase(ZEP), 9-cis-epoxycarotenoid dioxygenase (NCED), abscisic aldehyde oxidase (AAO), short-chain dehydrogenase/reductase-like(SDR), and cytochrome P450 in rice seedlings germinating from seeds implanted by ion beam for 72, 96, and 120 h after imbibitions (HAI) were determined by real-time PCR. Moreover, we also explored the changes of endogenous ABA content in rice seedlings after 48, 72, 96, 120, and 144 h after imbibitions using enzyme-linked immunosorbent assay (ELISA). The results showed that ion beam implantation could enhance the genes' transcription activity which was involved in ABA biosynthesis. However, the response of each gene is not consistent with the underlying differences in ion flux. The obviously up-regulated expression of ZEP, AAO2, SDR, and P450-2 were observed underlying the behaviour at an ion flux of 1 x 10(17) N+/cm(2). However, the expression of NCED, AAO1, and SDR2 can be enhanced by 5 x 10(17) N+/cm(2). The expression of AAO3, SDR1, and P450-1 can be elevated underlying the both ion flux of 1 x 10(17) N+/cm(2) and 5 x 10(17) N+/cm(2). The expression of SDR3 can be enhanced in every ion flux. The results of ELISA showed that endogenous ABA level in rice seedlings increased at treatment with vacuum, 1 x 10(17) and 5 x 10(17) N+/cm(2). Collectively, ion beam irritation can enhance the expression of genes involved in ABA biosynthesis, resulting in increasing content of endogenous ABA in rice. Our findings suggest that ABA pathway was involved in the adaption to irradiation with ion beam in plants.