Palythoa heliodiscus is a zoantharian (family Sphenopidae) found in shallow tropical reef environments, forming encrusting colonial mats with polyps incorporating foreign particles into the coenenchyme. The species belongs to the palytoxin-producing clade of Palythoa and is of interest for marine natural products research. Its genomic data contribute to understanding palytoxin biosynthesis, zoantharian systematics, and the competitive ecology of encrusting reef organisms.