Aim: The relationship of population genetics with the ecology and biogeography of species may be explored by comparing phenotypically similar but ecologically different congeners with overlapping ranges. We compared genetic differentiation between two congeneric rocky intertidal gastropods across a major portion of their sympatric range. We hypothesized that the habitat generalist with high abundance and continuous distribution would exhibit comparatively less genetic differentiation than the habitat specialist with low abundance and a fragmented distribution. Location: Northeast Atlantic from the northwest Iberian Peninsula to southern British coastline. Taxon: Gastropoda, Trochidae, Steromphala (formerly Gibbula) Methods: Field surveys were conducted to assess presence/absence and abundance of Steromphala umbilicalis (generalist) and S. pennanti (specialist) at 23 localities along ~1800 km coastline. We isolated polymorphic microsatellite markers for both species (seven loci for S. umbilicalis and eight for S. pennanti) and used these to genotype 187 S. umbilicalis and 157 S. pennanti individuals. We used standard population genetic analyses to compare patterns of genetic differentiation between species in relation to the field surveys. Results: Steromphala pennanti showed a more fragmented distribution, significantly lower abundance, and greater genetic differentiation than S. umbilicalis. One S. umbilicalis population towards the north of the range (southern Britain) was genetically distinct from all other sampled populations. Steromphala pennanti showed greater genetic differentiation between three southern localities, which may be attributable to its fragmented distribution and lower abundance because of limited availability of its preferred fucoid habitat in this region. We also suggest that oceanographic currents could be associated with regional genetic structure. Main conclusions: The habitat generalist showed high local abundances, continuous distribution and low regional genetic differentiation across much of its range. We found the opposite pattern for the habitat specialist. Our study highlights the importance of considering ecological (e.g. abundance, habitat preferences) and abiotic variables (e.g. ocean currents and temperature) for understanding differences in genetic structure of sympatrically distributed congeners.