As a component of the photosynthetic apparatus in cyanobacteria, the phycobilisome (PBS) plays an important role in harvesting and transferring light energy to the core photosynthetic reaction centers. The size, composition (phycobiliprotein and chromophore), and assembly of PBSs can be dynamic to cope with tuning photosynthesis and associated cellular fitness in variable light environments. Here, we explore the role of PBS-related stress responses by analyzing deletion mutants of
cpcF
or
cpcG1
genes in
Synechocystis
sp. PCC 6803. The
cpcF
gene encodes a lyase that links the phycocyanobilin (PCB) chromophore to the alpha subunit of phycocyanin (PC), a central phycobiliprotein (PBP) in PBSs. Deletion of
cpcF
(i.e., Δ
cpcF
strain) resulted in slow growth, reduced greening, elevated reactive oxygen species (ROS) levels, together with an elevated accumulation of a stress-related Peroxiredoxin protein (Sll1621). Additionally, Δ
cpcF
exhibited reduced sensitivity to a photosynthesis-related stress inducer, methyl viologen (MV), which disrupts electron transfer. The
cpcG1
gene encodes a linker protein that serves to connect PC to the core PBP allophycocyanin. A deletion mutant of
cpcG1
(i.e.,Δ
cpcG1
) exhibited delayed growth, a defect in pigmentation, reduced accumulation of ROS, and insensitivity to MV treatment. By comparison, Δ
cpcF
and Δ
cpcG1
exhibited similarity in growth, pigmentation, and stress responses; yet, these strains showed distinct phenotypes for ROS accumulation, sensitivity to MV and Sll1621 accumulation. Our data emphasize an importance of the regulation of PBS structure in ROS-mediated stress responses that impact successful growth and development in cyanobacteria.