Our aim is to understand and integrate the molecular, biochemical, physiological and ecological responses of plants in the field to factors of global climate change. This research used Free Air-gas Concentration Enrichment (FACE) technology to enrich [CO2] and [O3] to levels predicted for 2050, in a soybean agro-ecosystem. This ecosystem is a good model for studying plant responses to climate change because it is a relatively homogeneous growing environment and all plants in the canopy are genetically identical. This increases the power of the experiment to detect subtle treatment effects and facilitates investigation of the molecular and biochemical factors underlying physiological and ecological responses. We used the Affymetrix soybean microarray to investigate the response of over 37,000 genes to changes in [CO2] and [O3] across the growing season. A significant challenge of microarray experiments is interpreting the results in a biologically relevant context. In order to meet this challenge, we have adapted visualization software originally written for Arabidopsis thaliana. We have also developed high-throughput biochemical and enzymatic assays to allow analysis of the many samples needed to meaningfully assess treatment effects given background variation. One important mechanism by which plants cope with global atmospheric change is the oxidative stress response. Damage caused at the cellular level by oxidative stress feeds forward to decrease leaf photosynthesis and therefore canopy and ecosystem productivity. The antioxidant system consists of enzyme cycles and metabolite pools that maintain a balanced redox state. Total antioxidant capacity in leaves increases over the growing season, regardless of growth [CO2] or [O3]. Changes in the redox state of the ascorbate pool are observed in plants challenged with elevated [O3]. We are integrating these results with changes in antioxidant transcripts and enzymes to provide a mechanistic analysis of the response of the plant antioxidant system to global change.