Giant clams (Family: Cardiidae) are integral to reef structures, providing food and habitat to other organisms, but are threatened by climate change and overharvesting. They rely on supplemental nutrition through photosymbiosis, and evidence shows that harbouring multiple photosymbionts may help them withstand fluctuating conditions. Globally, giant clams have been found to associate with photosymbionts of the genera Symbiodinium, Cladocopium, Durusdinium, and Gerakladium, however, this has not previously been investigated in Western Australian. Using a DNA metabarcoding approach, the nuclear ribosomal Internal Transcribed Spacer region 2 (ITS2) was targeted to amplify Symbiodiniaceae in four giant clam host species – Hippopus hippopus, Tridacna maxima, Tridacna noae and Tridacna squamosa. Within 78 samples, 103 unique Amplicon Sequence Variants (ASVs) were identified, representing 14 ITS2 types of Symbiodiniaceae. All host species harboured a combination of Symbiodinium, Cladocopium and Durusdinium, while only T. maxima hosted Gerakladium. Symbiodinium dominated (>50% relative abundance) the Tridacna hosts, while Cladocopium dominated H. hippopus. Photosymbiont assemblages differed across spatial scales, with higher diversity observed in offshore reefs. Harbouring a combination of symbionts, including Durusdinium, the ‘extremophile’, may enhance the resilience of giant clams, improve their ability to withstand environmental change and secure their future in reef ecosystems.