Upon protoolytle treatment of thylakoid membranes, extrinsic proteins are selectively degraded. The remaining resistant proteins have been analyzed by SDS-PAGE. In the thylakoids of Chlamydomonas reinhardii, six polypeptides or protein fragments of 20 kD or higher are resistant to proteolysis. These intrinsic proteins have been identified as: the apoproteins of the chlorophyll-protein complexes CP I and LHCP; a polypeptide whose presence is related to the chlorophyll b content of the cells; and a portion of a chloroplast-made 34 kD polypeptide. Furthermore, after proteolytic treatment of the membranes, the LHCP complex can be resolved into two subcomplexes, apparently differing in their polypeptide composition.