To study the interaction of the nuclear and chloroplast genomes in the biogenesis of the photosynthetic apparatus, nuclear mutants of Chlamydomonas reinhardtii deficient in photosystem II (PSII) activity were analyzed. Two independently-isolated, allelic nuclear mutants show a pleiotropic reduction in a set of functionally related PSII polypeptides. Immunoblot analysis reveals that the two mutants, nac-1-18 and nac-1-11, accumulate reduced amounts of the chloroplast-encoded polypeptides P5 and P6 and are completely deficient in polypeptides D1 and D2. Polypeptides of the oxygen-evolving and light-harvesting complexes associated with PSII, however, are present at wild-type levels. Analysis of mRNAs encoding PSII polypeptides from these mutants indicates that all messages are present, although some species, including the D2 message, are significantly elevated. When mutant cells are pulse-labeled for 10 min with [C]acetate, a greatly reduced amount of labeled D2 protein is observed, while all other PSII polypeptides are synthesized normally. These data indicate that the mutations present in nac-1-18 and nac-1-11 affect a nuclear gene whose product specifically controls the translation and/or degradation of the chloroplast-encoded D2 polypeptide.