Comparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors which limit dispersal and/or drive divergence, aiding conservation management. By RAD-sequencing 214 European lobsters (Homarus gammarus) from 32 locations, and 349 European spiny lobsters (Palinurus elephas) from 15 locations, we isolated 6,340 and 7,681 SNP loci, respectively, and used these data to characterise contemporary population structuring and investigate potential spatial and environmental drivers of genomic heterogeneity.