Photoautotrophic organisms depend on the ambient light for their growth and viability; therefore, it is not surprising that they utilize sophisticated light-regulated signaling systems to acclimate to variable light environments. Cyanobacteria are important primary producers that perform oxygenic photosynthesis in various environmental niches. Cyanobacterial genomes encode multiple and diverse photoreceptors which are often connected to second messenger signaling networks. Here, we review the current knowledge of light-regulated second messenger signaling in cyanobacteria, focusing on two examples: cyclic di-GMP signaling systems for regulation of Thermosynechococcus sessility and Synechocystis motility. We also briefly introduce the present research on various nucleotide second messenger molecules, such as cAMP, cGMP, cyclic di-GMP, cyclic di-AMP, and the alarmone (p)ppGpp in cyanobacteria. In natural conditions, incident light contains a lot of different information on wavelength, intensity, and time scales. Further understanding of second messenger signaling in cyanobacteria will uncover how cyanobacteria extract the crucial information from their light environment to regulate cellular responses of ecophysiological importance.