The Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) can form under oxidizing conditions a supramolecular complex with the regulatory protein CP12. Both GAPDH and PRK activities are inhibited within the complex, but they can be fully restored by reduced thioredoxins (TRXs). We have investigated the interactions of eight different chloroplast thioredoxin isoforms (TRX f1, m1, m2, m3, m4, y1, y2, x) with GAPDH (A4, B4, and B8 isoforms), PRK and CP12 (isoform 2), all from Arabidopsis thaliana. In the complex, both A4-GAPDH and PRK were promptly activated by TRX f1, or more slowly by TRXs m1 and m2, but all other TRXs were in-effective. Free PRK was regulated by TRX f1, m1, or m2, while B4- and B8-GAPDH were absolutely specific for TRX f1. In-terestingly, reductive activation of PRK caged in the complex was much faster than reductive activation of free oxidized PRK, and activation of A4-GAPDH in the complex was much faster (and less demanding in terms of reducing potential) than activation of free oxidized B4- or B8-GAPDH. It is proposed that CP12-assembled supramolecular complex may represent a reservoir of inhibited enzymes ready to be released in fully active conformation following reduction and dissociation of the complex by TRXs upon the shift from dark to low light. On the contrary, autonomous redox-modulation of GAPDH (B-containing isoforms) would be more suited to conditions of very active photosynthesis.