Helicolenus dactylopterus is an Atlantic benthopelagic fish species inhabiting high-energy habitats on continental slopes, seamounts and islands. Partial sequences of the mitochondrial control region (D-loop) and cytochrome b (cyt b) were used to test the hypothesis that H. dactylopterus disperses between continental margin, island and seamount habitats on intraregional, regional and oceanic scales in the North Atlantic. Individuals were collected from five different geographical areas: Azores, Madeira, Portugal (Peniche), Cape Verde and the northwest Atlantic. D-loop (415 bp) and cyt b (423 bp) regions were partially sequenced for 208 and 212 individuals, respectively. Analysis of variation among mitochondrial DNA sequences based on pairwise F-statistics and AMOVA demonstrated marked genetic differentiation between populations in different geographical regions specifically the Mid-Atlantic Ridge (Azores)/northeast Atlantic (Portugal, Madeira) compared to populations around the Cape Verde Islands and in the northwest Atlantic. Some evidence of intraregional genetic differentiation between populations was found. Minimum-spanning network analysis revealed star-shaped patterns suggesting that populations had undergone expansion following bottlenecks and/or they have been colonized by jump dispersal events across large geographical distances along pathways of major ocean currents. Mismatch distribution analysis indicated that Azores and northwest Atlantic populations fitted a model of historical population expansion following a bottleneck/founder event estimated to be between 0.64 and 1.2 million years ago (Ma).