Microarray analysis indicated low-O(2) conditions resulted in upregulation of psbA1, the normally low-abundance transcript that encodes the D1' protein of photosystem II in Synechocystis sp. PCC 6803. Using a DeltapsbA2:DeltapsbA3 strain, we show the psbA1 transcript is translated and the resultant D1' is inserted into functional PSII complexes. Two other cyanobacterial strains have psbA genes that were induced by low oxygen. In two of the three strains examined, psbA was part of an upregulated gene cluster including an alternative Rieske iron-sulfur protein. We conclude this cluster may represent an important adaptation to changing O(2) levels that cyanobacteria experience.