The supramolecular organization of membrane proteins (MPs) is sensitive to environmental changes in photosynthetic organisms. Isolation of MP supercomplexes from the green algae , which are believed to contribute to cyclic electron flow (CEF) between the cytochrome complex (Cyt- ) and photosystem I (PSI), proved difficult. We were unable to isolate a supercomplex containing both Cyt- and PSI because in our hands, most of Cyt- did not comigrate in sucrose density gradients, even upon using chemical cross-linkers or amphipol substitution of detergents. Assisted by independent affinity purification and MS approaches, we utilized disintegrating MP assemblies and demonstrated that the algae-specific CEF effector proteins PETO and ANR1 are Cyt- interactors, with ANR1 requiring the presence of an additional, presently unknown, protein. We narrowed down the Cyt- interface, where PETO is loosely attached to cytochrome and to a stromal region of subunit IV, which also contains phosphorylation sites for the STT7 kinase.