Coral reefs around the world are under the threat of global and regional stressors. Studying the molecular responses of corals to environmental stressors may help develop biomarkers of coral health and provide data for informed management decisions. With the rapid advance in DNA sequencing technology, it is now feasible to generate a huge amount of genomic data to support functional genomic studies of coral disease and stress responses with a moderate amount of funding. In this study, we aimed to sequence the transcriptome and organize the sequence data into a searchable database for the brain coral Platygyra carnosus, a structure forming dominant species along the coast of southern China.