Cladopsammia gracilis (Dendrophylliidae), an ahermatypic coral, was sampled in the Sanya Bay in the South China sea. According to skeletal based taxonomy, the genus Cladopsammia is characterized by its phaceloid growth form of corallites basally united with common coenosteum, and well developed Pourtales plan. With both skeletal morphology and mitochondrial study, our samples were identified as Cladopsammia gracilis. In the research, we assembled an genome. The gff and fasta files of conding genes, non-coding genes, repeat sequecnes were provided here.