The plausibility of trait divergence under divergent natural selection in the presence of gene flow in natural populations is a contentious issue in evolutionary research. Its importance lies in the fact that this process is thought to be one of the key triggers in ecological speciation in which a species splits into ecologically distinct forms when separate niches are occupied. In this study we demonstrate strong genetic divergence at the IDH1 locus between pond- and canal-inhabiting individuals of the salt marsh beetle Pogonus chalceus from the Guérande salt fields. Moreover, wing size, a trait that has a heritable basis in this species, was significantly larger in the pond populations, which is in concordance with the unstable nature of this habitat. The relationship between IDH1 allele frequencies and wing size variation was consistent with patterns seen across western European populations. By means of neutral allozymes and microsatellites we detected a small but significant degree of sexual isolation between ecotypes. We conclude that speciation is ongoing and that divergence reflects a balance between selection and gene flow.