Between March 2018 and September 2019, 286 adult individuals of the honeycomb worm Sabellaria alveolata were sampled from 17 intertidal locations covering the species' full latitudinal distribution from Morocco to Northern UK. Thoracic tissues were preserved in guanidine thiocyanate buffer for genomic DNA extraction. DNA was digested using the Alf-I enzyme, and 2b-RAD libraries were constructed by ligation of Illumina Nextera sequencing adapters and PCR amplification. Final pooled libraries were sequenced on an Illumina NextSeq550 platform (a pilot run, plus five full sequencing runs in total) at the Centre Hospitalier Regional et Universitaire Morvan (Brest, France). The dataset was generated to support analyses of genetic diversity, connectivity, and adaptive variation in relation to environmental conditions.