We studied the variation at 30 anonymous and 30 expressed sequence tag (EST)-associated microsatellites in 4 natural populations of turbot Scophthalmus maximus living in habitats with different salinity and temperature conditions. We identified putative divergent selection effects on 3 genes: the fibroblast growth factor receptor, the β microglobuline, and the trap alpha gene for translocon associate protein. The markers closely linked to these genes showed significant deviations from the neutral expectations using 2 different statistical methods in several pairwise population comparisons involving samples from salty and brackish environments. Our results confirmed the weak genetic structure among populations from the northeast Atlantic and the low but significant genetic differentiation of turbot from the Baltic Sea. These results suggest that populations from the Baltic–Atlantic transition area could be accumulating adaptive polymorphisms in the face of high gene flow This work was funded by the grant PGIDIT06PXIB261178PR from Xunta de Galicia, a Consolider Ingenio Aquagenomics project (CSD2007-00002) from Spanish Ministry of Education and Science, and an Isidro Parga Pondal Fellowship to R.V. SI