Six chlorophyll-containing bands were observed upon electrophoretic analysis of Anacystis nidulans thylakoid membranes. These ranged in apparent molecular weights from approximately 360 to 45 kdalton. Measurements of the light absorption and chlorophyll fluorescence properties of these bands revealed numerous differences among the aggregates. The larger chlorophyll-protein complexes had a chlorophyll absorption maximum at 676 nm while the smallest band, band VI, at approximately 45 kdalton, absorbed at 668 nm. The chlorophyll-protein organization of four submembrane particles was also examined. Digitonin and N-tetradecyl-N,N-dimethyl-3-ammonio-1-pro-panesulfonate were used to fractionate thylakoids and each treatment yielded two green fractions after sucrose density gradient centrifugation. The upper green fractions of both procedures were enriched in band VI. In addition, these fractions showed low temperature fluorescence emission at 686 nm. Conversely, the lower green fractions were enriched in the larger bands (bands I and II), and yielded fluorescence emission at 696 and 716 nm. The gel electrophoresis analysis of these chlorophyll-protein bands revealed 11 peptides ranging in size from less than 10 to 64 kdaltons. The larger CP bands contained as many as five to six polypeptides, whereas band VI contained only two species (at 45 and 48 kdalton). These data suggest that the only proteins in band V (approximately 75 kdalton) and band VI are the chlorophyll binding proteins for photosystems I and II, respectively. We present a model which correlates chlorophyll-protein organization and specific fluorescence emission peaks. Central to this model is the interaction of the larger chlorophyll-protein complexes with bands V and VI to yield fluorescence at 696 and 716 nm, respectively. In addition, the polypeptide composition of each complex allows us to construct a topological model of these complexes within the Anacystis thylakoid.