Coral reef trophodynamics is extremely complex and still poorly understood, while investigated for decades. Recent advances on organic matter sources, fluxes, trophic niches of species, and spatiotemporal variations of food webs are first summarized. Then, tools used in trophodynamics research are briefly documented, from traditional pioneer methods of stomach content analysis to more recent biochemical methods (stable isotopes, fatty acids, biochemical composition, metabolomics, DNA metabarcoding, etc.) and modeling approaches. Eventually, future challenges and perspectives are presented addressing the diverse scenarios of coral reef trophic functioning response in front of the ongoing changes in global and local stressors.