Abstract The genus Platygyra represents an essential group of reef-building corals in marine ecosystems. Here, we present the first high-quality genome assembly of the brain coral Platygyra daedalea, a widespread species known for its ecological resilience across diverse marine environments. Using long-read sequencing combined with chromosomal-level scaffolding based on a genetic linkage map, we assembled an 878.6 Mb genome with a contig N50 of 34.8 Mb (7.C.Q66).