Genetic variation was assessed in Atlantic wolffish, Anarhichas lupus, across the North Atlantic Ocean using microsatellite and amplified fragment length polymorphism (AFLP) markers. Despite unusual life history attributes such as large benthic eggs, large larvae, a limited pelagic stage and relatively sedentary adults, which suggest potential for strong population structure, range-wide FST values were comparable to other marine fishes (≤0.035). Nevertheless, both significant genetic differentiation among regions and isolation by distance were observed, suggesting limited dispersal in this species. AFLP loci, evaluated on a subset of samples, revealed slightly higher FST values, but similar patterns of differentiation and isolation-by-distance estimates, compared to microsatellites. The genetic structure of Atlantic wolffish has likely been shaped by its post-glacial history of recolonization, North Atlantic current patterns and continuity of habitat on continental shelves.