AimMost animal species live in spatially and temporally heterogeneous landscapes where resources are unevenly distributed. Consequently, individuals must adapt their migratory behaviour to optimize feeding and breeding opportunities. Here, we assess the role of life-history (anadromy) and seascape (a derivation of the concept of landscape) heterogeneity on the genetic connectivity of coastal brown trout populations (Salmo trutta L., 1758). LocationEnglish Channel. MethodsA causal modelling approach, combining geographical data with inferences on gene flow among 20 populations, deploying neutral microsatellite markers, was used to identify environmental factors influencing brown trout genetic dispersal between rivers. Alternative models of landscape permeability combining least-cost path and transect analysis were employed. The model selection procedure was based on a multiple regression analysis on distance matrices analysis (MRDM) and a linear mixed modelling approach using maximum likelihood population effects (MLPE). ResultsLandscape genetic analyses showed a hierarchical genetic structure with two main genetic units corresponding to the eastern and western marine ecoregions of the English Channel delineated by the Cotentin peninsula. Within these two regions, a model, which included parameters for depth and seabed substrate habitat features, explained significantly more variance in genetic differentiation than simple isolation-by-distance models alone. Main conclusionsThe genetic structure of brown trout populations within the English Channel appears to be shaped by the spatial arrangement and quality (with respect to feeding opportunities) of marine habitats, which promotes a clinal variation in migratory behaviour, which in turn determines the level of gene flow among neighbouring streams. Genetic structure thus partly reflects microgeographical responses to spatial variation in foraging conditions at sea. These results show that the marine environment, rarely considered previously, has an important role in combination with variation in freshwater environments in the evolution of life history in migratory aquatic animals.