To fill the gap and provide a representation of responses across different fish species to elevated CO2 in their natural habitat, we sequenced brain transcriptomes of five adult damselfish species (Ac. polyacanthus, Amblyglyphidodon curacao, D. aruanus, Pomacentrus adelus, and P. moluccensis) and a cardinal fish species (Apogon compressus) from a coral reef at a natural CO2 seep and control sites in Papua New Guinea.