Dinoflagellates are a group of marine microorganisms that possess not only aberrant nucleus, but also many unique characteristics. Photosynthetic dinoflagellate Symbiodinium form mutualistic symbiosis with corals and a number of marine microbes to maintain metabolite interaction and nutritional exchanges among these holobiont members for relatively nutrient-rich homeostasis in the oligotrophic marine environment. When we are facing the massive devastation of marine coral reefs worldwide, it is of critical importance to understand the mechanism of coral bleaching and seek a way to rescue the coral reefs which are blue carbon sink for global CO₂ cycle and habitats of 25% ocean creatures. In this review, dinoflagellate biology will be briefly described, and then the symbiosis of coral and dinoflagellate Symbiodinium will be investigated in which the special light guiding structure in corals is seen to enhance the coral photon trapping and thus to amplify the dinoflagellate photosynthesis. Photo systems II and I in dinoflagellate Symbiodinium will be discussed for their functions in cell growth and metabolism, followed by their viability determination with the chlorophyll fluorescence measurement. The environmental impact on the dinoflagellate photosynthesis will be explored within the context of climate change. At the end, future research directions involving newly emerging coral cell lines and single cell study using microfluidics for the interaction and symbiosis in coral holobiont will be addressed.