In several cyanobacteria,petH, the gene encoding ferredoxin:NADP oxidoreductase (FNR), is transcribed from at least two promoters depending on growth conditions. Two transcripts (short and long) are translated from two different translation initiation sites, resulting in two isoforms (large and small, respectively). Here, we show that inSynechocystisPCC6803 the global transcriptional regulator NtcA activates transcription from the distalpetHpromoter. Modification of the NtcA-binding site prevents NtcA binding to the promoterin vitroand abolishes accumulation of the small isoform of FNRin vivo. We also demonstrate that a similarpetHtranscription and translation regime occurs in other cyanobacteria. The conditions under which this system operates provide hints for the function of each FNR isoform.