(A.R., I.V.) Oxygenic photosynthesis evolved with cyanobacteria, the ancestors of plant chloroplasts. The highly oxidizing chemistry of water splitting required concomitant evolution of efficient photoprotection mechanisms to safeguard the photosynthetic machinery. The role of flavodiiron proteins (FDPs), originally called A-type flavoproteins or Flvs, in this context has only recently been appreciated. Cyanobacterial FDPs constitute a specific protein group that evolved to protect oxygenic photosynthesis. There are four FDPs in Synechocystis sp. PCC 6803 (Flv1 to Flv4). Two of them, Flv2 and Flv4, are encoded by an operon together with a Sll0218 protein.Their expression, tightly regulated by CO 2 levels, is also influenced by changes in light intensity. Here we describe the overexpression of the flv4-2 operon in Synechocystis sp. PCC 6803 and demonstrate that it results in improved photochemistry of PSII. The flv4-2/OE mutant is more resistant to photoinhibition of PSII and exhibits a more oxidized state of the plastoquinone pool and reduced production of singlet oxygen compared with control strains. Results of biophysical measurements indicate that the flv4-2 operon functions in an alternative electron transfer pathway from PSII, and thus alleviates PSII excitation pressure by channeling up to 30% of PSII-originated electrons. Furthermore, intact phycobilisomes are required for stable expression of the flv4-2 operon genes and for the Flv2/Flv4 heterodimer-mediated electron transfer mechanism. The latter operates in photoprotection in a complementary way with the orange carotenoid protein-related nonphotochemical quenching. Expression of the flv4-2 operon and exchange of the D1 forms in PSII centers upon light stress, on the contrary, are mutually exclusive photoprotection strategies among cyanobacteria.Photosynthetic light reactions are evolutionarily highly conserved among oxygenic photosynthetic organisms from cyanobacteria to higher plants. Because of dangerous chemistry of the water splitting reactions, oxygenic photosynthesis produces reactive oxygen species (ROS) and other radicals that potentially could destroy the photosynthetic machinery. To avoid permanent damage, all oxygenic photosynthetic organisms are equipped with an array of various photoprotective and regulatory mechanisms. Accumulating evidence on these regulatory mechanisms has revealed vast evolutionary differences between organisms performing oxygenic photosynthesis.Photosynthetic organisms have a capacity to adjust to different light intensities and to changes in the availability of electron sinks, which depends largely on metabolic cues. When light or metabolic conditions change, photosystems can dissipate excess energy as heat in nonphotochemical energy dissipation processes in the light-harvesting antenna systems (for review, see Horton et al., 1996;Müller et al., 2001). Cyanobacteria have phycobilisomes (PBs) as light-harvesting antenna, which also participate in state transitions (for review, see van Thor et al., 1998;Mullineaux ...