Photosynthesis is a series of redox reactions, in which several electron transport processes operate to provide the energetic balance of light harvesting. In addition to linear electron flow, which ensures the basic functions of photosynthetic productivity and carbon fixation, alternative electron transport pathways operate, such as the cyclic electron flow (CEF), which play a role in the fine tuning of photosynthesis and balancing the ATP/NADPH ratio under stress conditions. In this work, we characterized the electron transport processes in microalgae species that have high relevance in applied research and industry (e.g., , , , sp.) by using flash-induced fluorescence relaxation kinetics. We found that a wave phenomenon appeared in the fluorescence relaxation profiles of microalgae to different extents; it was remarkable in the red cells of , and , but it was absent in green cells of and . Furthermore, in microalgae, unlike in cyanobacteria, the appearance of the wave required the partial decrease in the activity of Photosystem II, because the relatively high Photosystem II/Photosystem I ratio in microalgae prevented the enhanced oxidation of the plastoquinone pool. The wave phenomenon was shown to be related to the antimycin A-sensitive pathway of CEF in but not in other species. Therefore, the fluorescence wave phenomenon appears to be a species-specific indicator of the redox reactions of the plastoquinone pool and certain pathways of cyclic electron flow.