Transcriptional responses to heat stress were assayed in early life-history stages of 11 crosses between and amongst Acropora tenuis colonies originating from reefs along the Great Barrier Reef. We identified a single nucleotide polymorphism outlier (Fst=0.89) between populations in the unannotated gene Acropora25324, which exhibited constitutively higher gene expression in populations with dams originating from Curd reef, a far north, warm adapted inshore reef, suggesting an important role of this gene in adaptation to warmer environments. Further, juveniles exposed to heat and in symbiosis with heat-evolved Symbiodiniaceae displayed intermediate transcriptional responses between its progenitor taxa (Cladocopium goreaui) and the more stress tolerant Durusdinium trenchii, indicating that the development of heat tolerance acquisition is potentially a conserved evolutionary process in Symbiodiniaceae. These findings reveal the underlying mechanisms, and for the first time, their relative contribution, of coral responses to climate change and provide a foundation for optimizing conservation methods like assistant gene flow. Overall design: crosses were generated from gametes collected from 5 populations across the Great Barrier Reef. Larvae from these crosses were sampled prior to experimentation ("Pre") and then set up into two treatments ("Control temperature", and "Heat stress"). Following experimentation, pools of larvae were sampled for RNAseq from both treatments for each cross. Remaining larvae from each cross was settled to the juvenile phase and exposed to either control or ambient temperature conditions. Further, juveniles were exposed to one of four symbiont uptake treatments. Juveniles were sampled following the experiment for RNA-seq