In this study, the tolerance to salt stress of the photosynthetic machinery was examined in relation to the effects of the genetic enhancement of the unsaturation of fatty acids in membrane lipids in wild-type and desA+ cells of Synechococcus sp. PCC 7942. Wild-type cells synthesized saturated and mono-unsaturated fatty acids, whereas desA+ cells, which had been transformed with the desA gene for the Delta12 acyl-lipid desaturase of Synechocystis sp. PCC 6803, also synthesized di-unsaturated fatty acids. Incubation of wild-type and desA+ cells with 0.5 M NaCl resulted in the rapid loss of the activities of photosystem I, photosystem II, and the Na+/H+ antiport system both in light and in darkness. However, desA+ cells were more tolerant to salt stress and osmotic stress than the wild-type cells. The extent of the recovery of the various photosynthetic activities from the effects of 0.5 M NaCl was much greater in desA+ cells than in wild-type cells. The photosystem II activity of thylakoid membranes from desA+ cells was more resistant to 0.5 M NaCl than that of membranes from wild-type cells. These results demonstrated that the genetically engineered increase in unsaturation of fatty acids in membrane lipids significantly enhanced the tolerance of the photosynthetic machinery to salt stress. The enhanced tolerance was due both to the increased resistance of the photosynthetic machinery to the salt-induced damage and to the increased ability of desA+ cells to repair the photosynthetic and Na+/H+ antiport systems.