This study investigated metabolic responses in Synechocystis sp. strain PCC 6803 to photosynthetic impairment. We used 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU; a photosystem II inhibitor) to block O 2 evolution and ATP/NADPH generation by linear electron flow. Based on 13 C-metabolic flux analysis ( 13 C-MFA) and RNA sequencing, we have found that Synechocystis sp. PCC 6803 employs a unique photoheterotrophic metabolism. First, glucose catabolism forms a cyclic route that includes the oxidative pentose phosphate (OPP) pathway and the glucose-6-phosphate isomerase (PGI) reaction. Glucose-6-phosphate is extensively degraded by the OPP pathway for NADPH production and is replenished by the reversed PGI reaction. Second, the Calvin cycle is not fully functional, but RubisCO continues to fix CO 2 and synthesize 3-phosphoglycerate. Third, the relative flux through the complete tricarboxylic acid (TCA) cycle and succinate dehydrogenase is small under heterotrophic conditions, indicating that the newly discovered cyanobacterial TCA cycle (via the ␥-aminobutyric acid pathway or ␣-ketoglutarate decarboxylase/succinic semialdehyde dehydrogenase) plays a minimal role in energy metabolism. Fourth, NAD(P)H oxidation and the cyclic electron flow (CEF) around photosystem I are the two main ATP sources, and the CEF accounts for at least 40% of total ATP generation from photoheterotrophic metabolism (without considering maintenance loss). This study not only demonstrates a new topology for carbohydrate oxidation but also provides quantitative insights into metabolic bioenergetics in cyanobacteria. C yanobacteria, which first appeared in shallow marine settings as early as 3 billion years ago (1, 2), are now widely distributed in diverse nutrient and light environments (3-5). They can perform oxygenic photosynthesis and respiration simultaneously in the same compartment (6, 7). Cyanobacteria contain two photosystems to harvest light energy. Photosystem II (PSII) splits water and transports electrons sequentially through plastoquinone (PQ), cytochrome b 6 f, plastocyanin, and photosystem I (PSI), forming a linear electron flow (LEF) to produce ATP and NADPH. Alternatively, a cyclic electron flow (CEF) runs around PSI to generate ATP (8, 9). The cyanobacterial CEF involves respiratory electron transport reactions and PSI enzymes. NAD(P)H dehydrogenase complex (NDH-1) oxidizes NADPH and provides electrons for the PQ pool. Then the electrons from PQ flow to PSI and ferredoxin to regenerate NADPH via ferredoxin-NADP ϩ reductase (FNR). The CEF can regulate ATP and NADPH ratios for CO 2 fixation and respiration in plants (10). Cyanobacteria have a much larger PSI content than plants. For example, the PSI/PSII ratio in Synechocystis sp. strain PCC 6803 is about 5, suggesting the significant role of PSI in energy metabolism (6). To decipher photosynthesis mechanisms, researchers often use the herbicide 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) to block the PQ binding site of PSII so that the LEF is inactivated. Under DCMU treatm...