The photosystem (PS) II antenna system comprises several biochemically and spectroscopically distinct complexes, including light-harvesting complex 11 (LHCII), chlorophyll-protein complex (CP) 29, CP26, and CP24. LHCII, the most abundant of these, is both structurally and functionally diverse. The photosynthetic apparatus is laterally segregated within the thylakoid membrane into PSI-rich and PSII-rich domains, and the distribution of antenna complexes between these domains has implications for antenna function. We report a detailed analysis of the differences in the polypeptide composition of LHCII, CP29, and CP26 complexes associated with grana and stroma thylakoid fractions from spinach (Spinacia oleracea L.), making use of a very high-resolution denaturing gel system, coupled with immunoblots using monospecific antibodies to identify specific antenna components. We first show that the polypeptide composition of the PSII antenna system is more complex than previously thought. We resolved at least five type I LHCII apoproteins and two to three type 11 LHCII apoproteins. We also resolved at least two apoproteins each for CP29 and CP26. In state 1-adapted grana and stroma thylakoid membranes, the spectrum of LHCII apoproteins is surprisingly similar. However, in addition to overall quantitative differences, we saw subtle but reproducible qualitative differences in the spectrum of LHCII apoproteins in grana and stroma membrane domains, including two forms of the major type 11 apoprotein. The implications of these findings for models of PSII antenna function in spinach are discussed.Most of the Chl in the thylakoid membrane of higher plants and green algae is bound by specialized antenna complexes associated with either PSI or PSII (5,15,33 Chl. The CP29 complex has a Chl a/b ratio of 2.2 to 2.5 (5, 27) and has an apoprotein several kD larger than those of the LHCII complex. CP26 also has a higher Chl a/b ratio than LHCII but generally comigrates with LHCII in both native and fully denaturing SDS-PAGE systems (4, 27). Coupled with the difficulty in separating CP29 from the LHCII apoproteins in some species (particularly in spinach [16,17]), this has contributed to confusion in the literature as to the identities of these two complexes. This issue has recently been settled by the comparison of partial protein sequence data for CP29 and CP26 in barley (Hordeum vulgare) with a full-length gene sequence for CP29 (26), confirming that CP29 and CP26 are distinct complexes, both from each other and from LHCII.In this paper we will use the terms CP26 and CP29 as defined in ref. 4. Little is known for certain about the physical arrangement of the PSII antenna system, but the isolation of 02-evolving complexes lacking LHCII but still containing CP29 suggests that CP29 is more closely associated with the reaction center (9). The gel systems used in ref. 9 did not distinguish between CP29 and CP26; therefore, no conclusions could be drawn about the relationship of CP26 to the reaction center.