Abstract
Endosymbiotic dinoflagellates (Symbiodiniaceae) influence coral thermal tolerance at both local and regional scales. In isolation, the effects of host genetics, environment, and thermal disturbances on symbiont communities are well understood, yet their combined effects remain poorly resolved. Here, we investigate Symbiodiniaceae across 1300 km in Australia's Coral Sea Marine Park to disentangle these interactive effects. We identified Symbiodiniaceae to species‐level resolution for three coral species ( Acropora cf humilis, Pocillopora verrucosa , and Pocillopora meandrina ) by sequencing two genetic markers of the symbiont (ITS2 and psbA ncr ), paired with genotype‐by‐sequencing of the coral host (DArT‐seq). Our samples predominantly returned sequences from the genus Cladocopium , where Acropora cf humilis affiliated with C3k, Pocillopora verrucosa with C. pacificum , and Pocillopora meandrina with C. latusorum . Multivariate analyses revealed that Acropora symbionts were driven strongly by local environment and thermal disturbances. In contrast, Pocillopora symbiont communities were both partitioned 2.5‐fold more by host genetic structure than by environmental structure. Among the two Pocillopora species, the effects of environment and host genetics explained four times more variation in symbionts for P. meandrina than P. verrucosa. The concurrent bleaching event in 2020 had variable impacts on symbiont communities, consistent with patterns in P. verrucosa and A. cf humilis , but not P. meandrina . Our findings demonstrate how symbiont macroscale community structure responses to environmental gradients depend on host species and their respective population structure. Integrating host, symbiont, and environmental data will help forecast the adaptive potential of corals and their symbionts amidst a rapidly changing environment.