This dataset provides amplicon sequence variant (ASV) counts of Antarctic deep-water sponges (Demospongiae and Hexactinellida), bottom water samples and sediment collected for microbiome analysis during expeditions PS96 (RV Polarstern, 2015/16) and JR17003a (RRS James Clark Ross, 2018) in the Weddell Sea. The 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.The table gives the feature IDs (unique identifier for each ASV), the counts for each ASV in each sample, and total counts for each ASV. The first line includes the sample IDs for sponge, seawater, and sediment samples. Sample IDs for sponges are composed of abbreviations for sponge species: Anoxycalyx joubini (Aj), Inflatella belli (Ib), Isodictya lankesteri (Il), Rossella fibulata (Rf), Rossella nuda (Rn), Rossella racovitzae (Rr), Rossella vanhoeffeni (Rv), Tentorium semisuberites (Ts), and the field ID of each specimen. Sample IDs for seawater (sw) and sediment (sed) indicate the respective station.