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Previous studies have shown that live cyanobacteria can produce photocurrent in bio-photoelectrochemical cells (BPEC) that can be exploited for clean renewable energy production. Electron transfer from cyanobacteria to the electrochemical cell was proposed to be facilitated by small molecule(s) mediator(s) whose identity (or identities) remain unknown. Here, we elucidate the mechanism of electron transfer in the BPEC by identifying the major electron mediator as NADPH in three cyanobacterial species. We show that an increase in the concentration of NADPH secreted into the extracellular medium (ECM) is obtained by both illumination and activation of the BPEC. Elimination of NADPH in the ECM abrogates the photocurrent while addition of exogenous NADP+ significantly increases and prolongs the photocurrent production. NADP+ is thus the first non-toxic, water soluble electron mediator that can functionally link photosynthetic cells to an energy conversion system and may serve to improve the performance of future BPECs.