Two chlorophyll-protein complexes associated with photosystem II (PSII) of the cyanobacterium Anacystis nidulans R2 have been detected. The larger of the two complexes, CPVI-1, contained a 71-kDa and a 42-kDa protein. The 71-kDa protein was determined to be the anchor protein of the phycobilisomes (the light-harvesting complex of A. nidulans PSII), since it was recognized by an antibody raised against a similar protein from another cyanobacterium. The second complex, CPVI-4, contained a previously unobserved 36-kDa chlorophyll-binding protein. Additionally, two other PSII chlorophyll-protein bands were characterized. CPVI-2 contained a 52-kDa band that was recognized by an antibody raised against the presumptive PSII reaction center protein of Chlamydomonas reinhardtii. It gave rise to a fluorescence emission peak (77K) at 695 nm, indicating that this chlorophyll-protein complex may harbor the reaction center of PSII. Finally, CPVI-3 was found to have a 45-kDa protein and to be immunologically related to the presumptive immediate-antenna protein of the C. reinhardtii PSII.