Speciation requires the acquisition of reproductive isolation, and the circumstances under which this could evolve are of great interest. Are new species formed after the acquisition of generalized incompatibility arising between physically separated populations, or may they arise as a result of the action of disruptive selection beginning with the divergence of a rather restricted set of gene loci? Here we apply the technique of amplified fragment length polymorphism (AFLP) analysis to an intertidal snail whose populations display a cline in shell shape across vertical gradients on rocky shores. We compare the FST values for 306 AFLP loci with the distribution of FST estimated from a simulation model using values of mutation and migration derived from the data. We find that about 5% of these loci show greater differentiation than expected, providing evidence of the effects of selection across the cline, either direct or indirect through linkage. This is consistent with expectations from nonallopatric speciation models that propose an initial divergence of a small part of the genome driven by strong disruptive selection while divergence at other loci is prevented by gene flow. However, the pattern could also be the result of differential introgression after secondary contact.