Abstract: Cold acclimation of cyanobacteria involves the regulation of many genes, such as crhR that encodes RNA helicase. In this study, the transcription of crhR was examined in Synechocystis sp. PCC 6803 transferred from 30oC to 15oC, and its transient expression was found within 2h. Inactivation of this gene in the cyanobacterium led to loss of growth at 15oC, great reduction of photosynthetic and respiratory activities, and inability to eliminate lipid peroxides. Overexpression of crhR from PrbcL in the crhR mutant fully complemented the mutation, and the complemented strain showed slightly improved growth at 15oC compared to the wild type. In the wild type, temperature downshift induced the up-regulation of fatty acid desaturase genes desA, desB and desD and the increase of unsaturation degree of fatty acids. In the crhR mutant, the induction of desB by temperature downshift was significantly reduced, and the contents of polyunsaturated fatty acids were not increased under the same conditions. It is proposed that crhR may directly affect protein synthesis in the cyanobacterium under low-temperature stress, or indirectly, exert its effects on enzyme activities by regulating the expression of chaperone genes