Plastocyanin, encoded by the petE gene, can transfer electrons to photosystem I (PSI) and cytochrome c oxidase during photosynthetic and respiratory metabolism in cyanobacteria. We constructed a petE mutant of Synechocystis sp. strain PCC 6803 and investigated its phenotypic properties under different light conditions. When cultured under continuous light, inactivation of petE accelerated the plastoquinone pool reoxidation, slowed the reoxidation rate of the primary quinone-type acceptor, and decreased the connectivity factor between the individual photosystem II (PSII) photosynthetic units. Compared with the wild-type control, the petE mutant showed a decrease in its PSI/PSII fluorescence ratio and an increase in its dark respiration rate. When cultured under a light–dark photoperiod, the petE mutation caused an increase in the phycocyanin to chlorophyll ratio. Consequently, the mutant line was a darker blue than its wild-type counterpart. Moreover, the petE mutation increased the efficiency of light capture, nonphotochemical quenching, and linear electron transport activity, but decreased the functional absorption cross section of PSII. These results suggest that plastocyanin is involved in regulating the redox state of the photosynthetic electron transfer chain, and the petE mutation can induce interesting phenotypic properties that are specific to the light–dark photoperiod.