Coral reefs depend upon a functional symbiosis between cnidarian hosts and unicellular dinoflagellate algae of the family Symbiodinidaceae. Exaiptasia sp., a genus of globally distributed sea anemone, have become an important model system for cnidarian-dinoflagellate endosymbioses and the role of the microbiome in affecting metaorganism biology and adaptive capacity. Here we sequenced and assembled the genome of the Aiptasia model, strain F003.