Coral reefs globally are being impacted by ocean warming and marine heatwaves caused by climate change, resulting in the loss and degradation of these ecologically and economically important ecosystems. Although predictions for the fate of corals into the future are relatively grim, some optimism can be found in the range of responses to elevated temperatures exhibited among different coral species and regions. We explored the natural variability in thermal tolerance using three species of scleractinian corals (Pocillopora acuta, Acropora nana, and Porties lutea) sourced from reefs with distinct thermal regimes (variable vs. stable) in southern Taiwan. We monitored the seasonal dynamics of the holobiont lipidome and Symbiodiniaceae genera over the course of 15- months to assess baseline data of primary energy provision sources. This in-situ study revealed site-specific Symbiodiniaceae genera associations, whereby a higher proportion of corals from the thermally variable reef site hosted the more heat-resistant genus, Durusdinium; no site differences were found for the holobiont lipidome. Building upon this we conducted a lab-based experiment, using the same species and sites, to assess coral response to chronic moderate warming (30˚C), and then acute high temperature exposure (32˚C). In general, corals showed adequate to good performance under the chronic warming scenario but experienced substantial bleaching under the higher acute temperature. Lastly, we explored the potential capacity for active enhancement of coral thermal tolerance through assisted evolution (via transgenerational acclimation) in Pocillopora acuta. We found that thermally conditioned adult colonies reproduced earlier in the lunar cycle and had smaller offspring with lower photosynthetic efficiency than offspring sourced from colonies held at a control temperature. We did not find evidence of improved thermal performance in offspring sourced from heated parent colonies when exposed to elevated temperatures. Collectively, the finite natural upper temperature limits of corals and the lack of evidence for enhanced thermal tolerance via transgenerational acclimation highlight the need for urgent action to mitigate climate change to ensure the persistence of healthy coral reefs into the future.