This study contains RAD-sequencing data generated for the hydrothermal vent gastropod Ifremeria nautilei. RAD-sequencing libraries were constructed at the Station Biologique de Roscoff, France, in the ANR CERBERUS project. Individual ddRAD libraries were constructed according to the protocol available in dx.doi.org/10.17504/protocols.io.bv4tn8wn. Briefly, genomic DNA from each samples were extracted and quantified, then double-digested with two restriction enzymes, ligated to adaptors, and PCR-amplified to yield Illumina compatible fragments. All individuals were then pooled equally in a single library that was then size-selected and subjected to quality control before Illumina HiSeq4000 PE150 sequencing at the Genoscope, in the eDNAbyss umbrella project.