Genetic analysis of the allele interactions was carried out with the use of recombinant plasmids and reporter genes to study the autorepressor function of prqR, which negatively regulates the prqR-prqA operon and the response to oxidative stress inductor methyl viologen (MV) in cyanobacterium Synechocystis sp. PCC 6803. The wild-type (WT) prqR showed negative autoregulation and suppressed in trans the derepressed mutant alleles. Frameshift mutation C134fs, which was introduced in prqR by site-directed mutagenesis, impaired the autoregulation, implicating the C-terminal domain in transcriptional repression by PrqR. Missense mutation C134S altering the only redox-sensitive Cys of PrqR, had no effect on prqR expression, indicating that oxidation and consequent disulfide bridging of two PrqR molecules was not responsible for MV-induced autorepression of prqR. Analysis of the prqR-prqA deletion derivatives lacking the promoter and most of prqR revealed weak uncontrollable expression of reporter cat, testifying to the existence of a constitutive promoter in prqA responsible for MV resistance. The interaction of the WT and mutant prqR alleles in Synechocystis cells revealed a cis-dominant character of the alteration of prqR autoregulation. Stimulation of in cis autorepression of prqR was assumed to contribute to the induction of systems protecting cyanobacteria from oxidative stress.