Minnows of the genus Phoxinus are promising candidates to investigate adaptive divergence, as they inhabit both still and running waters of a variety of altitudes and climatic zones in Europe. We used landmark-based geometric morphometric methods to quantify the level of morphological variability in Phoxinus populations from streams and lakes of Northern Italy and the Danube basin. We analyzed body shape differences of populations in the dorsal, lateral, and ventral planes, using a large array of landmarks and semilandmarks. As the species identification of Phoxinus on morphological characters is ambiguous, we used two mitochondrial genes to determine the genetic background of the samples and to ensure we are comparing homogenous groups. We have found significant body shape differences between habitats: Minnow populations inhabiting streams had a deeper body and caudal peduncle and more laterally inserted pectoral fins than minnows inhabiting lakes. We have also found significant body shape differences between genetic groups: Italian minnows had deeper bodies, deeper and shorter caudal peduncles, and a shorter and wider gape than both groups from the Danube. Our results show that the morphology of Phoxinus is highly influenced by habitat and that body shape variation between habitats was within the same range as between genetic groups. These morphological differences are possibly linked to different modes of swimming and foraging in the respective habitats and are likely results of phenotypic plasticity. However, differences in shape and interlandmark distances between the groups suggest that some (though few) morphometric characters might be useful for separating Phoxinus species.