This dataset contains 482 short read samples from many sites covering the species' ranges of the rough periwinkles Littorina saxatilis, Littorina arcana, and Littorina compressa. Littorina saxatilis samples are further subdivided into four ecotypes (Wave, Crab, Brackish and Barnacle) and an additional category for unassigned snails. Eight samples were collected from each site, species and ecotype, with a roughly even split of males and females. All samples were whole genome shotgun sequenced to a target of 10X coverage. Sequencing was split among two sequencing centres (137 samples with GeneWiz and 345 with Liverpool Centre for Genomic Research). Each samples at Liverpool was sequenced in three separate runs because of library preparation errors. A few samples had to be replaced in subsequent runs.