In the context of rising seawater temperatures associated with climate change, the issue of whether coral holobionts deal with this challenge by shuffling their associations with stress- and/or heat-tolerant Symbiodinium, by generating heat-resistant host genotypes, or both is important for coral survival. In this study, the composition of communities of the endosymbiont Symbiodinium and the population genetics of the coral host Platygyra verweyi were examined in a reef impacted by hot-water discharged from the outlet of a nuclear power plant in operation in Kenting, Southern Taiwan since 1984. The water at this site is 2.0–3.0 °C warmer than adjacent reefs in summer, which have an average seawater temperature of 29.0 °C. The data were compared with those for the same species at other sites within 12 km of the outlet site. Platygyra verwyei was associated with one or both of Symbiodinium types C3 (heat sensitive) and D1a (heat tolerant) at all sites with the latter being the dominant at the nuclear power plant outlet. The proportion of C3 in populations increased gradually with increasing distance from the hot-water discharge. Genetic analysis of the Platygyra verweyi host using mitochondrial and nuclear markers showed no genetic differentiation among sites. Changes in the composition of Symbiodinium types associated with P. verweyi among closely located sites in Kenting suggested that this coral might have acclimatized to the constant thermal stress by selective association with heat-tolerant Symbiodinium types, whereas the role of the host in adaptation was inconclusive.