We present a genome assembly from a specimen of Mycale flammula (Porifera; Demospongiae; Poecilosclerida; Mycalidae). The genome sequence has a total length of 486.27 megabases. Most of the assembly (98.89%) is scaffolded into 16 chromosomal pseudomolecules. Five mitochondrial genome sequences were also assembled. From the metagenome data, we recovered six bins, of which one is a high-quality MAG. The metagenome bins were taxonomically assigned to Bacteroidia, Planctomycetia, Cyanobacteria and Gammaproteobacteria.