Microcystins are heptapeptide toxins produced by cyanobacteria. Microcystin-RR (MC-RR) is a common variant among the 80 variants identified so far. There have been many investigations documenting the toxic effects of microcystins on animals and higher plants, but little is known on the toxic effects of microcystins on algae, especially at molecular level. We studied the effects of MC-RR on gene expression profile of a few antioxidant enzymes and heat shock protein-70 (Hsp70) in Synechocystis sp. PCC6803. After two days post-exposure, a high dose toxin (5 mg/l, about 4.8 × 10⁻³ mM) significantly increased expression levels of the genes gpx1, sodB, katG, acnB, γ-TMT and dnaK2, while a relatively low dose toxin (1 mg/l, about 9.63 × 10⁻⁴ mM) induced a moderate and slow increase of gene expression. Our results indicate that MC-RR could induce the oxidative stress in Synechocystis sp. PCC6803 and the increase in gene expression of antioxidant enzymes and Hsp70 might protect the organism from the oxidative damage. In addition, cell aggregation was observed during the early period of exposure, which might be a specific oxidative stress reaction to MC-RR.