The cytological organization of de novo photosystem II biogenesis in chloroplasts was examined using a unique technique of cellular subfractionation. The cellular subfractions were biochemically examined for three chloroplast membrane compartments. The results revealed membranes that are specialized in the synthesis of photosystem II proteins that are encoded by the chloroplast genome and synthesized by bacterial-like ribosomes within this semiautonomous organelle. Furthermore, a novel class of envelope membrane was identified which has a higher density than envelope membrane that was previously described. The localization of newly synthesized proteins and lipids after cellular subfractionation were also determined. Similarly, intermediates of chlorophyll synthesis were localized in the cellular subfractions, and it was confirmed that they are not only localized to the envelope membrane. The results reveal novel membranes that are involved in the synthesis of chloroplast genome-encoded subunits of photosystem II and the import of chloroplast proteins from the cytosol. They also contribute to the current realization in the field that organelles are highly compartmentalized and that certain compartments are specialized in biogenesis processes.