Background: The in vivo radiation-induced bystander effects (RIBE) at the developmental, genetic, and epigenetic levels have been well demonstrated using model plant Arabidopsis thaliana (A. thaliana). However, the mechanisms underlying RIBE in plants are not clear, especially lacking a comprehensive knowledge about the genes and biological pathways involved in the RIBE in plants. Materials and Methods: A high-density oligonucleotide probe-based cDNA microarray was used to analyze transcriptomic response in aerial leaf tissues of A. thaliana seedlings at 24 h after root exposure to 10 Gy of α-irradiation. Results: The root-localized irradiation resulted in up-regulated expressions of 238 genes and down-regulated expressions of 42 genes in bystander aerial tissues with a ≥ 2.0-fold difference and < 0.05 p-values. The high frequency of gene families for up-regulated expressions were glutathione S-transferases, cytochrome P450 enzyme, the ethylene response factor, and the multidrug and toxic compound extrusion efflux, and for down-regulated expressions was the later embryogenesis abundant protein. Moreover, there were 200 up-regulated genes and 183 down-regulated genes with 1.5–2.0-fold expression changes. Conclusion: In addition to the canonical IR-induced genes, some genes that are not previously linked to radiobiological effects were found to be involved in RIBE in plants.