Symbiotic relationships involving photosynthetic dinoflagellates (Symbiodiniaceae) are integral to the survival and adaptability of reefs globally. Using the ITS2 marker and SymPortal framework, we characterised the endosymbiont communities of two native giant clams, Tridacna crocea and T. squamosa, across four intertidal sites in Singapore. Environmental parameters (light, temperature, sedimentation and hydrodynamic activity) were also measured to identify associations with endosymbiont assemblages. Additionally, we contextualised these giant clam-based compositions against the endosymbiotic communities observed in other local reef species including hard corals and a nudibranch. Results revealed that giant clams predominantly hosted Symbiodiniaceae of genera Durusdinium and Cladocopium, with Symbiodinium in the background. Between species, T. crocea exhibited greater flexibility in its Symbiodiniaceae community. At sites showing marked differences in light intensity and hydrodynamic activity, distinct endosymbiont diversity levels were also observed. Comparisons among reef species similarly suggested a predominance of Durusdinium and Cladocopium, but the diversity of in hospite Symbiodiniaceae communities varied. This study is the first documentation of Symbiodiniaceae diversity in Singapore’s giant clams, and includes a reef-wide perspective of the Symbiodiniaceae assemblages in Singapore’s reefs. The findings enhance our understanding of the role of Symbiodiniaceae in coral reef resilience.