Algal symbionts are critical for the well-being of coral reefs. Dinoflagellates in the family Symbiodiniaceae establish a nutritional photosymbiosis with corals. Unfortunately, increasing marine heat waves break down symbioses between corals and Symbiodiniaceae. Therefore, surveys of Symbiodiniaceae diversity and evolutionary history are crucial to understand coral reef resilience. Traditional genetic markers uncovered the vast genetic diversity of Symbiodiniaceae but have limitations. We aim to establish novel genomic markers (UCEs) to study symbiont diversity and evolution.