Every cyanobacterial species contains genes encoding site-2-protease (S2P) homologues. The studied prokaryotic S2P homologues play essential roles in regulating stress responses through intramembrane proteolysis of membrane-bound anti-sigma factors. Here, the gene encoding Slr0643, one of four S2P homologues in Synechocystis sp. PCC 6803, was insertionally disrupted to explore its physiological role. Only a partially segregated mutant was obtained, indicating the essentiality of the gene product for growth. A pivotal role of fully functional Slr0643 in acid acclimation was demonstrated by defective acid acclimation to pH 6.5 in the mutant and transient induction of slr0643 in the wild-type after transfer from pH 7.5 to 6.5. DNA microarray and quantitative RT-PCR analyses of mutant and wild-type strains at pH 7.5 versus pH 6.5 identified genes involved in early acid acclimation and revealed genes expressed differentially due to slr0643 disruption. Early acid acclimation to pH 6.5 in the wild-type strain included upregulation of sigH, hik16 and hik35 and downregulation of pcrR and sigG, as well as downregulation of porins and upregulation of inorganic carbon and nitrogen transporters. The inability of the mutant strain to survive at pH 6.5 was found to be related to defective photosynthesis and excess expression of NADH dehydrogenase, together with excessive upregulation of carbon transporter and repression of nitrogen transporter and metabolism genes. Most interestingly, analysis of microarray data revealed the close relationship between slr0643 disruption and expression of the sigH operon. Thus it is suggested that Slr0643/Sll0857/SigH might act through an S2P/anti-Sigma factor/Sigma factor mechanism to play a role in acid acclimation.