As the global climate changes, plants will be challenged by environmental stresses that are more extreme and more frequent leading to increased yield loss. Specifically, ozone stress is an increasing problem in both urban and rural areas. Soybeans are one of the plant species that are quite ozone sensitive. The genetic mechanisms of response to ozone stress in soybeans are unclear and a good source of resistance in breeding stocks is lacking. We are working with two varieties of soybean, Fiskeby III (tolerant) and Mandarin (Ottawa, susceptible). We have collected and profiled transcripts (RNA-seq) from leaf tissues from both control and high ozone exposure at two time points. Illumina-based RNA-seq followed by a GO term enrichment was used to elucidate the differences in response mechanisms between varieties. Photosynthesis, stress response, and carbohydrate metabolism related GO terms are particularly enriched between the varieties at high ozone and within the same variety. The differences found in the GO enrichment analysis indicate that the differences in response between ozone tolerance and intolerance in Fiskeby is largely one of dosage of gene products and the timing of specific cellular responses to ozone exposure that limit or facilitate cell damage.