Dimethylsulfoniopropionate (DMSP) is a key compound in the marine sulfur cycle, and is produced in large quantities in coral reefs. In addition to Symbiodiniaceae, corals and associated bacteria have recently been shown to play a role in DMSP metabolism. Numerous ecological studies have focused on DMSP concentrations in corals, which led to the hypothesis that increases in DMSP levels might be a general response to stress. Here we used multiple species assemblages of three common Indo-Pacific holobionts, the scleractinian corals Pocillopora damicornis and Acropora cytherea, and the giant clam Tridacna maxima and examined the DMSP concentrations associated with each species within different assemblages and thermal conditions. Results showed that the concentration of DMSP in A. cytherea and T. maxima is modulated according to the complexity of species assemblages. To determine the potential importance of symbiotic dinoflagellates in DMSP production, we then explored the relative abundance of Symbiodiniaceae clades in relation to DMSP levels using metabarcoding, and found no significant correlation between these factors. Finally, this study also revealed the existence of homologs involved in DMSP production in giant clams, suggesting for the first time that, like corals, they may also contribute to DMSP production. Taken together, our results demonstrated that corals and giant clams play important roles in the sulfur cycle. Because DMSP production varies in response to specific species-environment interactions, this study offers new perspectives for future global sulfur cycling research.