Arabidopsis thaliana (At) ecotypes Columbia-0 (Col-0), Wassilewskija (WS), Cape Verde Islands (Cvi-0) and a relative, Thellungiella halophila (Th), were exposed to 20-25% over ambient ozone [O3] in a free air concentration enrichment (FACE) experiment (http://www.soyFACE. uiuc.edu), mirroring increases expected in the near future. Col-0 and WS accelerated development and developed lesions within 10 d under increased ozone, while Cvi-0 and Th grew slowly. RNAs were used in microarray hybridizations (Col-0-based 26 000 elements, 70-mer oligonucleotides). A two-step analysis of variance (ANOVA) model, including comparison with values obtained under [O3], was used for analyses. WS showed the greatest number of changes in gene expression in response to ozone. Th showed the least changes, suggesting that its expression state at [O3] was sufficient for resistance at increased ozone. Patterns observed in ambient air controls for Cvi-0 and Col-0 were most similar, while Th showed the greatest number of differences compared with the other controls. Compared with Col-0, however, Cvi-0 showed higher levels of expression of chaperones, receptor kinase-like and photosynthesis-related genes in ambient air. Cvi-0 exhibited ozone-mediated changes in a pathway involving AtSR, a homologue of the mammalian NF kappa B family of redox-sensitive transcription factors, changes in chaperones, WRKY and C2H2 proteins and antioxidants. WS displayed ozone-mediated decreases in the expression of two AtSR/NF kappa B family members, C2-domain proteins and genes associated with cell wall growth and changes in the expression of marker genes for programmed cell death (PCD), among them RCD1, a key regulator in this pathway. Microarray data were verified by reverse transcriptase (RT)-PCR. We relate O3-response diversity across the four lines to different responses among signaling and transcriptional response networks and differences in gene expression at [O3] levels.