In photosystem I, two electron-transfer pathways via quinones (A1A and A1B) are merged at the iron-sulfur Fe4S4 cluster FX into a single pathway toward the other two Fe4S4 clusters FA and FB. Using a quantum mechanical/molecular mechanical approach, we identify the redox-active Fe sites in the clusters. In FA and FB, the Fe site, which does not belong to the CxxCxxCxxxCP motif, serves as an electron acceptor/donor. FX has two independent electron acceptor Fe sites for A- and B-branch electron transfers, depending on the Asp-B575 protonation state, which causes the A1A-to-FX electron transfer to be uphill and the A1B-to-FX electron transfer to be downhill. The two asymmetric electron-transfer pathways from A1 to FX and the separation of the electron acceptor and donor Fe sites are likely associated with the specific role of FX in merging the two electron transfer pathways into the single pathway.