Mitochondria is the essential organelle for the production of cellular ATP in most eukaryotic cells, whether photosynthetic or not. It is widely studied, including in non-photosynthetic parasites such as trypanosomes, as a potential therapeutic target. We determined that many subunits of the respiratory complexes of Trypanosomes are shared with a non-parasitic photosynthetic species, Euglena gracilis. In this respect Euglena ancestor acquired its chloroplast by a secondary endosymbiotic event from a green primary eukaryotic alga. Structural analyzes have further highlighted unusual protein extra-structure associated with various respiratory complexes. Euglena gracilis is an historical microalga, being one the first protist described by microbiologists. Its photosynthesis has been broadly studied during the last century. One striking example is that Euglena was the organism studied by Melvin Calvin when he discovered the biochemical cycle which allow fixation of carbon dioxide into organic matter. In the frame of this project, we established a consolidated transcriptome of E. gracilis, which is a prerequisite to proper genome assembly and state of the art genetic manipulation. We then determined that most of the regulatory mechanisms of photosynthetic electron flow described so far in plants model organisms (Arabidopsis, Chlamydomonas) were not retained in Euglena gracilis. We then showed that original mechanisms (e.g. in terms of antennae composition or in terms of regulation of ATP/NADPH ratio) have been developed. In particular, we found that there is a strong coupling between respiration and photosynthesis. We then studied various strains of dinoflagellates originating not only from reef-building corals but also from soft octocorals, sea anemones, or even from giant clam from distant geographic locations (e.g. Hawai, Panama, Red sea, Japan). We determined the existence of three phenotyping groups with respect to regulatory mechanisms of photosynthetic electron transfer. This may have important ecological consequences due to the critical role of these processes on cellular energetic balance (including interactions between respiration and photosynthesis) and on the photoprotection capacity of cells. We Finally developed methodologies to study bioenergetics parameters in vivo in symbiosis (corals, anemones, jellyfish).