Light-dependen modification of photosynthetic pigmentation and cellular growth responses is commonly associated with increased fitness in photosynthetic organisms, including cyanobacteria. Prior analyses of pigmentation mutants in the freshwater cyanobacterium Fremyella diplosiphon has resulted in the observation that RcaE is a photosensor responsible for regulating organismal responses to changes in red light (RL) and green light (GL). RcaE regulates both pigmentation and cellular morphology, yet previous investigations and the analysis of additional pigmentation mutants here show that the signaling pathways regulating pigmentation and morphology appear to branch downstream of RcaE. We provide evidence that a Delta cpeR mutant has altered regulation of cellular morphology in addition to a known disruption in phycoerythrin synthesis. This marks the first description of the association of a regulator with the control of cellular morphology under both RL and GL in F. diplosiphon, apart from RcaE. In addition to providing a link between CpeR and the photoregulation of morphology in F. diplosiphon, the isolation of a Delta cpeR::IS66 mutant in the UTEX 481 strain represents both the first isolation of an IS66-based gene disruption and verification of the existence of an IS66-related element in F. diplosiphon. (C) 2011 Elsevier Inc. All rights reserved.