Exposure to methyl viologen in the presence of light facilitates the production of superoxide that gives severe damage on photosynthetic apparatus as well as many cellular processes in cyanobacteria and plants. The effects of methyl viologen on global gene expression of a unicellular cyanobacterium Synechocystis sp. strain PCC 6803 were determined by DNA microarray. The ORFs sll1621, slr1738, slr0074, slr0075, and slr0589 were significantly induced by treatment of methyl viologen for 15 min commonly under conditions of normal and high light. One of these genes, slr1738, which encodes a ferric uptake repressor (Fur)-type transcriptional regulator, is located divergently next to another induced gene, sll1621, in the genome. We deleted slr1738, and compared the global gene expression patterns of this mutant to that of wild type under non-stressed conditions. It was found that sll1621 was derepressed to the greatest extent, while many other genes including slr0589 but not slr0074 or slr0075 were derepressed to lesser extent in the mutant. Genetic disruption of sll1621, which encodes a putative type 2 peroxiredoxin, indicates that it is essential for aerobic phototrophic growth in both liquid and solid media in high light and on solid medium even in low light. Slr1738 was prepared as a His-tagged recombinant protein and shown to specifically bind to the intergenic region between sll1621 and slr1738. The binding was enhanced by dithiothreitol and abolished by hydrogen peroxide. We concluded that the Fur homolog, Slr1738, plays a regulatory role in the induction of a potent antioxidant gene, sll1621, in response to oxidative stress.