Abstract
<jats:p> Giant clams are some of the largest bivalve molluscs. They form a vital partnership with Symbiodiniaceae dinoflagellates that supply most of their energetic requirements. However, the factors that shape giant clam-associated photosymbiont communities remain unknown. Here, we profiled Symbiodiniaceae communities using ITS2 metabarcoding in eight giant clam species ( <jats:italic>Hippopus hippopus</jats:italic> , <jats:italic>H. porcellanus</jats:italic> , <jats:italic>Tridacna crocea</jats:italic> , <jats:italic>T. derasa</jats:italic> , <jats:italic>T. gigas</jats:italic> , <jats:italic>T. maxima</jats:italic> , <jats:italic>T. noae</jats:italic> and <jats:italic>T. squamosa</jats:italic> ) from 11 sites across the Philippine archipelago. Symbiodiniaceae community structure was shaped by an interplay between giant clam host and environment. Most giant clams were dominated by members of a single symbiont genus, with <jats:italic>Cladocopium</jats:italic> as the most prevalent, followed by <jats:italic>Durusdinium</jats:italic> and <jats:italic>Symbiodinium</jats:italic> . However, giant clam hosts also exhibited flexibility in their symbiotic partners that was evident across sites. Differences in giant clam-associated symbiont communities may contribute to differences in holobiont function and adaptability to variable environments. These findings deepen our understanding of giant clam-Symbiodiniaceae associations, offering a framework for predicting how giant clams may be affected by increasingly stressful reef conditions and, more importantly, informing strategies to improve mariculture and conservation practices. </jats:p>