Cassiopea andromeda is an ideal species for examining antioxidant stress response by non-calcifying zooxanthellate cnidarians because unlike its sister species Cassiopea xamachana, which is geographically restricted to Florida and the West Indies, C. andromeda typically occurs in tropical and subtropical waters worldwide. However, the molecular and cellular basis of antioxidant defences in Cassiopea species have largely been ignored but are fundamental to understanding the survival and distribution of these cnidarians, especially given that Cassiopea spp. themselves maybe useful indicators of marine ecosystem health in the face of increasing anthropogenic pollution and global climate change. Here we produced a high-quality draft genome sequence of C. andromeda that improves that will provide a foundational resource for advancing Cassiopea as a model research system for early diverging metazoans.