We present a genome assembly from a specimen of Cassiopea xamachana (upside-down jellyfish; Cnidaria; Scyphozoa; Rhizostomeae; Cassiopeidae). The genome sequence has a total length of 326.12 megabases. Most of the assembly (98.3%) is scaffolded into 20 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.34 kilobases. From the metagenome data, we recovered one medium-quality bacterial bin assigned to Endozoicomonas sp.