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Ferredoxins (FDXs) are ubiquitous proteins that bind iron-sulfur (Fe-S) clusters and usually catalyse electron transfer reactions. In eukaryotic photosynthetic organisms, a relatively high number of [2Fe-2S] cluster-containing FDXs is present in plastids and mitochondria. These are mostly redox-active FDXs, except one mitochondrial FDX that no longer binds an Fe-S cluster and is a component of the respiratory complex I. We have performed a phylogenomic study to describe the content and distribution of FDXs in different phylogenetic groups of the Archaeplastida clade, including the two models Arabidopsis thaliana and Chlamydomonas reinhardtii. Important differences exist since the number of FDXs ranges from four to 19. From the sequence characteristics and phylogenetic analyses, they cluster in 10 clades: eight containing plastidial FDXs and two mitochondrial FDXs. Six clades are present in most organisms, while four clades comprising plastidial FDXs (FDX5, FDX7, FDX8, and FDX9) are present in a small subset of organisms, mostly algae and lower Embryophytes; the FDX5 and FDX9 clades are even only present in Chlorophyceae. The expression patterns of these two FDXs in Chlamydomonas combined with the physiological and biochemical studies performed with FDX5 suggest specific roles of FDX5 in anoxia and of FDX9 in the dark. Structural analyses provide additional support to the functional divergence among plastidial FDXs. Overall, these analyses revealed the existence of an important diversity within the FDX family and allowed refining the FDX classification in Archaeplastida. It also provides clues for future physiological analyses to decipher the functions of the uncharacterised FDXs.