We present a genome assembly from a specimen of Nausithoe racemosa (coronate scyphozoan jellyfish; Cnidaria; Scyphozoa; Coronatae; Nausithoidae). The assembly contains two haplotypes with total lengths of 4 784.66 megabases and 4 868.20 megabases. Most of haplotype 1 (97.34%) is scaffolded into 20 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 13.97 kilobases. From the metagenome data, we recovered one high-quality metagenome-assembled genome.