The photosynthetic apparatus of a mutant of Chlamydomonas reinhardtii, hf-9, impaired in fatty acid desaturation at the ω6 position of fatty acids of chloroplasts was investigated. Measurement of photosynthetic activities revealed that both PS I and PS II activities were reduced in hf-9. However, little alteration occurred in the contents and subunit assemblies of the PS I complex, PS II core complex and light-harvesting complex of PS II. Lipids bound to these chlorophyll-protein (CP) complexes in hf-9 were shown to contain decreased levels of 16:4(4,7,10,13) and 18:3(9,12,15), with accumulation of 16:1(7) and 18:1(9), as compared with in the parent. Highly unsaturated fatty acids of chloroplast lipids may be required for the normal functions of PS I and PS II, by associating with these complexes.