Coral resilience to thermal stress relies in part on the composition of their symbiotic community, which includes algal symbionts in the Family Symbiodiniaceae and members of the microbiome living within the coral host. Because corals are long-lived and sessile, modulating their symbiotic communities may play an important role in acclimatization to distinct environments. Corals living in environments with higher levels of diel thermal variability (DTV) have been shown to exhibit increased thermal tolerance; however, little is known about how DTV structures coral symbiont communities. In this study, three inshore and three offshore reef sites in Bocas del Toro, Panama that differ in their DTV were used to investigate the structure of symbiotic communities of the reef-building coral Siderastrea siderea. Metabarcoding of the ITS2 (algal) and 16S (microbial) loci allowed for comparison of community diversity and abundances of symbionts between inshore and offshore reefs, which differ in their DTV. We found abundances and composition of both ITS2 and 16S communities were significantly different between inshore and offshore reefs. Specifically, algae in the genus Durusdinium were found to be more prevalent in offshore populations while Cladocopium were more abundant inshore, suggesting that different levels of DTV experienced on these reefs might drive differences in the algal communities hosted by S. siderea in this region. Additionally, three bacterial indicator species were identified as potential biomarkers of thermal variability. We conclude that divergent DTV experienced on inshore and offshore reefs plays a role in structuring symbiotic communities of S. siderea.