First choromosome-level genome assembly of the sponge Halisarca dujardinii (well-known for its unusual ability of regeneration even from single cell suspension). The dataset includes genome assembly, mitochondrion, annotations of repeats, protein-coding genes, tRNAs, rRNAs, mitochondrial genome annotation. As well, we provide functional annotation of predicted peptides. This functional annotation includes results of BLASTP and BLASTX searches against SwissProt database, PFAM domains, homology prediction by EggNOG-mapper, signal peptides and transmembrane domains. Also the repository includes the code used to create the dataset. For more detailed information see "readme" and "annotation usage notes" files included in the repository.