Cyanothece sp. strain ATCC 51142, a unicellular, diazotrophic cyanobacterium, demonstrated extensive metabolic periodicities of photosynthesis, respiration, and nitrogen fixation when grown under N2-fixing conditions. This report describes the relationship of the biosynthesis of photosynthesis genes to changes in the oligomerization state of the photosystems. Transcripts of the psbA gene family, encoding the photosystem II (PSII) reaction center protein D1, accumulated primarily during the light period, and net transcription reached a peak between 2 to 6 h in the light in light-dark (LD) growth and between 4 to 10 h in the subjective light when grown under continuous light (LL). The relative amount of the D1 protein (form 1 versus form 2) appeared to change during this diurnal cycle, along with changes in the PSII monomer/dimer ratio. D1 form 1 accumulated at approximately equal levels throughout the 24-h cycle, whereas D1 form 2 accumulated at significantly higher levels at approximately 8 to 10 h in the light or subjective light. The psbD gene, encoding the reaction center protein D2, also demonstrated differences between the two copies of this gene, with one copy transcribed more heavily around 6 to 8 h in the light. Accumulation of the PSI reaction center proteins PsaA and PsaB was maximal in the dark or subjective-dark periods, a period during which PSI was primarily in the trimeric form. We conclude that photosystem organization changes during the diurnal cycle to favor either noncyclic electron flow, which leads to O2 evolution and CO2 fixation, or cyclic electron flow, which favors ATP synthesis.