We tested the thermal tolerance of coral larvae with heat-evolved and wild-type strains and explored the molecular mechanisms for the differential thermal tolerance with gene expression patterns. This archive provides the raw data of the RNA sequencing. Overall design: We sequenced the gene expression patterns of the coral host and the algal symbionts in hospite, dual RNA-seq. The sequencing was performed on a NovaSeq 6000 and yielding 2 billion reads. Each file contains data from the coral host and algal symbiont. For further methodological details please check the associated research paper (Science Advances).