Antioxidant isoenzymes function to eliminate free radicals and are localized to several different subcellular compartments within he plant cell. In Arabidopsis thaliana exposed to ozone (O-3), we have monitored the accumulation of mRNAs encoding both cytosolic and chloroplastic antioxidant isoenzymes. Two different O-3 exposure protocols yielded similar results. Upon O-3 exposure, the steady-state levels of three mRNAs encoding cytosolic antioxidant isoenzymes (ascorbate peroxidase, copper/zinc superoxide dismutase, and glutathione S-transferase) increase. The glutathione S-transferase mRNA responds very quickly to the oxidative stress (2-fold increase in 30 min) and is elevated to very high levels, especially in plants grown with a 16-h photoperiod. In contrast, O-3 exposure causes a decline in the levels of two chloroplastic antioxidant mRNAs (iron superoxide dismutase and glutathione reductase) and two photosynthetic protein mRNAs (chlorophyll a/b-binding protein and ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit). We show that this decline does not include all mRNAs encoding chloroplast-targeted proteins, since O-3 causes an elevation of mRNA encoding the chloroplast-localized tryptophan biosynthetic enzyme phosphoribosylanthranilate transferase. Two alternative hypotheses that could explain this differential mRNA accumulation in response to O-3 are discussed.