Natural selection can play an important role in the maintenance of genetic polymorphisms, despite ongoing gene flow. In the present study, we use previously analysed allozymic loci and perform an FST outlier-based analysis to detect the signatures of divergent selection between sympatric ecotypes of the marine snail Littorina saxatilis at different localities. The results obtained show that different allozyme polymorphisms are affected (directly or indirectly) by selection at distinct geographical regions. The Phosmogluco mutase-2 locus was the best candidate for adaptation and further biochemical analyses were performed. The kinetic properties of the three more common genotypes of Pgm-2 were studied. The results obtained are concordant with two alternative hypotheses: (1) natural selection is acting directly on this locus or, more probably, (2) selection is affecting a genomic region tightly linked to the enzyme locus. In both cases, the known existence of a parallel and partially independent origin of these ecotypes would explain why different candidate loci were detected in different localities. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 225–233.