Abstract Cytochrome c 6 is a soluble electron carrier, present in all known cyanobacteria, that has been replaced by plastocyanin in plants. Despite their high structural differences, both proteins have been reported to be isofunctional in cyanobacteria and green algae, acting as alternative electron carriers from the cytochrome b 6 - f complex to photosystem I or terminal oxidases. We have investigated the subcellular localization of both cytochrome c 6 and plastocyanin in the heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 grown in the presence of combined nitrogen and under diazotrophic conditions. Our studies conclude that cytochrome c 6 is expressed at significant levels in heterocysts, even in the presence of copper, condition in which it is strongly repressed in vegetative cells. However, the copper-dependent regulation of plastocyanin is not altered in heterocysts. In addition, in heterocysts, cytochrome c 6 has shown to be the main soluble electron carrier to cytochrome c oxidase-2 in respiration. A cytochrome c 6 deletion mutant is unable to grow under diazotrophic conditions in the presence of copper, suggesting that cytochrome c 6 plays an essential role in the physiology of heterocysts that cannot be covered by plastocyanin. Graphical abstract Unlabelled Image Highlights • Cytochrome c 6 plays an essential role in the physiology of heterocyst that cannot be covered by plastocyanin. • Cytochrome c 6 is the main soluble electron donor to Cox2 in heterocysts. • Cytochrome c 6 is significantly expressed in the heterocyst in the presence of copper. [ABSTRACT FROM AUTHOR]