These data were generated in order to create a reference metagenome for the emerging model sponge species, Halichondria panicea and its microbiome. These data include raw sequences from three separate sequencing runs of the metagenome of a single individual of Halichondria panicea - one Illumina MiSeq (2x300 bp, paired-end, across two lanes) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Draft metagenome assemblies were created using the Illumina, ONT and both approaches combined. Metagenome assembled genomes (MAGs) for the sponge and two microbial symbionts were created from bining the Illumina-only metagenome assembly.