Metapopulation structure and genetic differentiation among subpopulations will be tightly related to patterns and processes of local adaptation and microevolution. Understanding the mechanisms behind genetic substructuring will aid in the interpretation of species’ ecological performances and strategies. The marine gastropod Littorina fabalis occurs in two size morphs – a small and a large – found in microhabitats of different wave exposure, but overlapping in distribution where wave exposure is intermediate. Earlier studies have found substantial genetic differentiation linked to morph in one allozyme locus (arginine kinase), while 29 other allozyme loci reveal no or minute differences between morphs. Here we add new results showing DNA variation in a RAPD marker being tightly linked to the allozyme variation. Indeed, 97% of the snails homozygotic for one of the Ark alleles had a unique DNA band, while 89% of the snails homozygotic for the other Ark allele lacked the marker. We discuss alternative hypotheses explaining the genetic substructure and suggest that the linkage of size, allozyme and DNA traits might be due to a paracentric chromosomal inversion involving loci coding for these traits. A genetic linkage of traits might promote microhabitat specialization of this species, and such a chromosomal transformation may therefore be adaptive. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 301–306.