This dataset was collected during the expedition 'SponGES0617' of research vessel Angeles Alvarino in 2017 to the Aviles Canyon System and the Le Danois Bank. It includes amplicon raw sequence reads (V3V4 region 16S rRNA gene survey) of seawater and deep-sea sponge-associated microbes. The sponge species Topsentia sp. and Phakellia hirondellei are covered. In addition to 16S sequences, also 18S, COI, and SNP data were generated for this sample set.