To attain a more profound insight into the molecular mechanisms underlying coral bleaching, we employed dual transcriptomics to analyze the gene expression profile of the ecologically valuable marine scleractinian coral, Seriatopora hytrix, across healthy, mild, and severely bleached states. These samples were collected by SCUBA diving off the coast of Sulawesi Island in the Republic of Indonesia. Our findings offer an encompassing comprehension of the molecular responses during natural environmental coral bleaching events, and underscore the significance of how the host can employ gene expression plasticity to ensure short-term survival and potential fitness enhancement in the face of future climate changes.