Hong Kong represents a subtropical, marginal marine environment characterized by diverse coral assemblages persisting near their environmental tolerance limits. These populations are hypothesized to have adapted to local stressors, establishing the region as a valuable natural laboratory for studying coral resilience. However, while recent bleaching episodes have increased in frequency, the proximate causes, often attributed to thermal stress and hyposalinity, remain unresolved. Furthermore, differential bleaching susceptibility and recovery patterns among local species are observed but largely unexplained. This laboratory study investigates the distinct acute and long-term physiological and molecular responses of Acropora digitifera (predominantly autotrophic) and Duncanopsammia peltata (predominantly heterotrophic) to examine the relative susceptibility and adaptive mechanisms of corals with contrasting trophic strategies under the individual and synergistic effects of heat stress and hyposalinity. By integrating physiological metrics with transcriptomic profiling of the coral holobiont, this research will elucidate the distinct molecular mechanisms underlying stress resistance and resilience among corals of different trophic strategies, in order to assess the vulnerability of subtropical coral communities to climate change, identify mechanisms supporting the future persistence of coral ecosystems in marginal environments, and inform restoration efforts by the prioritization of resilient corals as well as areas that may serve as trophic refugia.