Thioredoxin (Trx) is a small ubiquitous protein involved in the disulfide-dithiol exchange reaction occurring in cells and organelles. In vivo, Trx is reduced by Trx reductase using NADPH or photosynthetically produced reducing equivalents, and the reduced form Trx takes on the physiological functions. In the cyanobacterium Synechocystis sp. PCC6803, two Trx reductases, ferredoxin-Trx reductase (FTR) and NADPH-Trx reductase (NTR), and four typical Trx isoforms have been identified by genomic analysis. Based on analysis of the physiological features of the Trx reductase disruptants, we found that the NTR-Trx pathway is important for the antioxidant system, whereas the FTR-Trx pathway may play a more important role in the control of cell growth rate. In addition, by quantification of Trx abundance in the wild-type and the disruptant Synechocystis cells, we found that the gene product of slr0623, the homolog of m-type Trx in higher plants, is the most abundant Trx, and that accumulation of Trx isoforms occurs dependent on the expression of the other redox-related proteins. A study of the binary reducing equivalent pathways in cyanobacterial cells is reported here.