Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology and of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from geographic isolation (allopatry), isolation by distance (IBD), environment (IBE), adaptation (IBA), and time (IBT). We investigate how ecological and evolutionary processes influence genetic diversity and structure in 11 populations of pike (Esox lucius) using Restriction-site Associated DNA sequencing (RADseq). Study populations represented three ecotypes (freshwater, anadromous, and brackish water resident) along a latitudinal gradient (54.9 - 63.6 °N). Genetic diversity and structure were investigated both for the full RADseq dataset (5993 loci) and for an adaptive subset consisting outlier loci. Both neutral and adaptive processes influenced genetic structure, and their contributions differed between allopatric and sympatric populations, and also within and among ecotypes. Signatures of neutral processes were pronounced among geographically isolated freshwater populations, likely reflecting long time since divergence combined with low gene flow. For sympatric populations, ecotype (anadromous versus resident) and geography influenced both neutral and adaptive genetic structure, consistent with IBE. Outlier analyses pointed to a role of selection associated with salinity and temperature, consistent with IBA. Results provide rare evidence that separate analyses of neutral and adaptive loci can help illuminate how different, potentially interacting, processes jointly contribute to shaping spatiotemporal patterns of biodiversity. It is argued that data on adaptive rather than neutral genetic variation should inform management and policy development.