Phytobilins, linear tetrapyrrole pigments utilized for light-harvesting and light-sensing in photosynthetic organisms, are synthesized from biliverdin by ferredoxin-dependent bilin reductases (FDBRs) . We have determined the crystal structures of substrate-free and substrate-bound forms of PcyA, one such FDBR. These structures revealed the first tertiary structures of an FDBR family member. Based on these structures, we discuss the binding mechanisms of ferredoxin and substrate to PcyA. Moreover, we propose the reaction mechanism how PcyA controls the two-step reductions of biliverdin. Homology modeling of other FDBRs using PcyA structure may provide structural bases for the reaction mechanisms of other FDBRs.