Natural selection drives local adaptation, potentially even at small temporal and spatial scales. As a result, adaptive genetic and phenotypic divergence can occur among populations living in different habitats. We investigated patterns of differentiation between contrasting lake and stream habitats in the cyprinid fish European minnow (Phoxinus phoxinus) at both the morphological and genomic level using geometric morphometrics and AFLP markers, respectively. We also used a spatial correlative approach to identify AFLP loci associated with environmental variables representing potential selective forces responsible for adaptation to divergent habitats. Our results identified two morphotypes between lakes and streams, with lake fish presenting a deeper body and caudal peduncle compared to stream fish. Differences between these morphotypes conformed to a priori predictions concerning biomechanics and swimming performance in lakes versus streams. Moreover, morphological differentiation was found to be associated to several environmental variables, which could affect body and caudal peduncle shape. We found adaptive genetic divergence between these contrasting habitats in the form of a few "outlier" loci (2.9%) whose genetic divergence exceeded neutral expectations. We also detected additional loci (6.6%) not associated with habitat type (lake versus stream), but contributing to adaptive genetic divergence between populations. Specific environmental variables related to trophic dynamics, landscape topography and geography were associated with several neutral and outlier loci. These results provide new insights into the morphological divergence and genetic basis of adaptation to differentiated habitats in European minnows.