Collectively called zooxanthellae, photosynthetic dinoflagellates in the genus Symbiodinium are essential coral symbionts encompassing nine phylogenetic clades (A-I). The diversity and composition of zooxanthellae can fundamentally mediate coral responses to environmental change. For example, Symbiodinium in clade D is believed to be more thermally tolerant than its counterpart in clade C, and hence has the potential to convey thermal tolerance to the host coral. Yet, the physiological and molecular dynamics of symbiont changes underlying distinct coral responses upon environmental cues, remain largely unknown. In order to better understand the basal coral-zooxanthellae symbiotic responses to environmental perturbations, we conducted laboratory manipulative thermal stress experiments using freshly collected wild coral Pocillopora damicornis maintained in aquaria at ambient (26 °C) or elevated (32 °C) temperature, respectively. Based on our analysis of zooxanthellae density and genotypes, and the measurements of photosynthesis and calcification rates, we demonstrated that P. damicornis with dominant clade D Symbiodinium is much more robust to thermal stress relative to P. damicornis with dominant clade C Symbiodinium. This finding sheds new light on how symbiont shuffling could act as a defensive mechanism for increased coral resilience.