Description: Sponges (Porifera) host diverse and species-specific communities of microbial symbionts with which they maintain tight interactions. However, knowledge on the microbiomes of sponges from deep waters and remote polar areas is still scarce, especially for the sponge class Hexactinellida. Therefore, our aim was to describe the community composition, richness and density of microbial symbionts of Antarctic deep-water sponges, including several species of hexactinellids, and relate the findings to host ultrastructure and histology. During the Antarctic expeditions PS96 (RV Polarstern, 2015/16, eastern Weddell Sea) and JR17003a (RRS James Clark Ross, 2018, western Weddell Sea), 28 sponge specimens, bottom water and sediment were sampled for molecular analysis of microbial communities. The sponges were collected from deep habitats of 290-845 m by Bottom Trawl or Agassiz Trawl and comprised 19 hexactinellids and 9 demosponges. Bottom water was collected with a CTD rosette sampler which also measured environmental data (temperature, salinity, oxygen) close to the start or end point of the trawls and at four additional stations. Sediment was collected from the Agassiz trawl together with sponge samples during JR17003a. The molecular microbiome analysis targeted bacteria and was based on 16S rRNA gene sequencing of the V3-V4 variable regions. Sequences were processed using the QIIME2 environment. Amplicon sequence variants (ASVs) were generated with the DADA2 algorithm and classified based on the Silva 132 99% OTUs 16S database. Eight sponge specimens collected during JR17003a were further investigated microscopically for microbial symbionts, sponge histology and ultrastructure. Histological sections of 7-30 µm were stained in either Masson's trichrome or Hematoxylin/Eosin and images captured on a Zeiss Axioskop 2 plus with a QiCam camera using Northern Eclipse software. Ultrastructural sections of 60 nm were stained in uranyl acetate and lead citrate and then viewed and photographed with a Philips Morgagni transmission electron microscope equipped with a Gatan CCD camera. This Data Collection includes sampling information, environmental data, NCBI accession numbers and photographs of the analyzed sponges, data on the microbial symbiont communities (amplicon sequence variants and microbial phyla) of sponges, seawater and sediment, as well as micrographs of sponge histology and ultrastructure.