Cyanobacteria have versatile electron transfer pathways and many of the proteins involved are functional in both respiratory and photosynthetic electron transport. Examples of such proteins include the cytochrome b (6) f complex, NADH dehydrogenase and cytochrome oxidase complexes. In this study we have cloned and sequenced two gene clusters from the marine cyanobacterium Synechococcus sp. PCC 7002 that potentially encode heme-copper cytochrome oxidases. The ctaCIDIEI and ctaCIIDIIEII gene clusters are most similar to two related gene clusters found in the freshwater cyanobacterial strain Synechocystis sp. PCC 6803. Unlike Synechocystis sp. PCC 6803, Synechococcus sp. PCC 7002 does not have a cydAB-like gene cluster which encodes a quinol oxidase. The ctaCIDIEI and ctaCIIDIIEII gene clusters were transcribed polycistronically, although the levels of transcripts for the ctaCIIDIIEII gene cluster were lower than those of the ctaCIDIEI gene cluster. The ctaDI and ctaDII coding sequences were interrupted by interposon mutagenesis and full segregants were isolated and characterized for both single and double mutants. Growth rates, chlorophyll and carotenoid contents, oxygen consumption and oxygen evolution were examined in the wild type and mutant strains. Differences between the wild type and mutant strains observed in 77 K fluorescence spectra and in pulse-amplified modulated (PAM) fluorescence studies suggest that the cyanobacterial oxidases play a role in photoinhibition and high light tolerance in Synechococcus sp. PCC 7002.