Cyanobacteria are a group of prokaryotic organisms that perform oxygenic photosynthesis using a similar photosynthetic apparatus as is used in higher plants and eukaryotic algae. Cyanobacteria are also known to have a circadian rhythm. Here, we evaluated the effects on photosynthesis caused by the genetic manipulation of RpaA, which is a response regulator of a two-component regulatory system responsible for the signal output from circadian clocks. Using the unicellular cyanobacterium Synechocystis sp. PCC 6803, photosynthetic activities and transcript levels of photosystem I and photosystems II in the rpaA-overexpressing strain were measured, and it was found that the parameters, such as F-v/F-m, F-v'/F-m' qP, and Phi II , obtained from chlorophyll fluorescence analysis were decreased by rpaA overexpression. These results suggest that rpaA over-expression modified photosynthetic electron transport under normal light conditions. Thus, we demonstrated that RpaA regulates photosynthesis in cyanobacteria and can be a potential target of photosynthetic engineering in this cyanobacterium. (C) 2018, The Society for Biotechnology, Japan. All rights reserved.