Cyanobacteria are simple organisms which possess an endogenous circadian clock. Although the cyanobacterial clock has the same fundamental properties as circadian clocks in eukaryotes, its components are non-homologous to those of eukaryotes. The clock core of the cyanobacteria consists of the kai gene cluster and three Kai proteins KaiA, KaiB and KaiC, which the kai genes encode. The interactions among the Kai proteins modulate the phosphorylation state of KaiC, which generates circadian rhythm. The KaiC phosphorylation cycle constitutes the pacemaker of the cyanobacterial circadian rhythm. And signal transduction into and out of the clock core could occur via histidine protein kinase-based phosphorylation relays.