Within a plant cell, chloroplasts produce reactive oxygen species (ROS) at the highest rates. Singlet oxygen, superoxide anions and peroxides accumulate when the light intensity exceeds the capacity of the photosynthetic electron transport chain and metabolic electron consumption. Embedded in the heterotrophic cell, chloroplasts have a high-potential antioxidant defense system. The enzymatic components link to and substitute non-enzymatic protection by ascorbate and glutathione. Recent analysis demonstrated that the expressional regulation of the enzymatic components of the chloroplast antioxidant defense system is widely independent from regulation of extracellular antioxidant enzymes. It includes specific transcriptional regulation by differentially regulated transcription factors, post-transcriptional regulation by alternative splicing, complementary RNA and microRNAs and regulated protein-import into chloroplasts. Most chloroplast antioxidant enzymes show a high background expression activity, while it is low for most cytosolic components. Instead of the strong induction kinetic reported for cytosolic APx1 and APx2, most genes for chloroplast enzymes are two-directionally regulated in response to environmental signals. In this review an overview over the present state of knowledge on regulation of genes for chloroplast and extra-plastid antioxidant enzymes is provided based on the detailed analysis of model genes and comparison of transcriptome data.