The dinoflagellate algae, Symbiodiniaceae, are significant symbiotic partners of corals due to their photosynthetic capacity. The photosynthetic processes of the microalgae consist of linear electron transport, which provides the energetic balance of ATP and NADPH production for CO2fixation, and alternative electron transport pathways, including cyclic electron flow, which ensures the elevated ATP requirements under stress conditions. Flash-induced chlorophyll fluorescence relaxation is a non-invasive tool to assess the various electron transport pathways. A special case of fluorescence relaxation, the so-called wave phenomenon, was found to be associated with the activity of NAD(P)H dehydrogenase (NDH) in microalgae. We showed previously that the wave phenomenon existed in Symbiodiniaceae under acute heat stress and microaerobic conditions, however, the electron transport processes related to the wave phenomenon remained unknown. In this work, using various inhibitors, we show that (i) the linear electron transport has a crucial role in the formation of the wave, (ii) the inhibition of the donor side of Photosystem II did not induce the wave, whereas inhibition of the Calvin–Benson cycle accelerated it, (iii) the wave phenomenon was related to the operation of type II NDH (NDH-2). We therefore propose that the wave phenomenon is an important marker of the regulation of electron transport in Symbiodiniaceae.