The harbour porpoise Phocoena phocoena experiences high rates of incidental mortality in commercial fisheries, and in some areas these rates are sufficiently high to justify concern over population sustainability. Given this high mortality, conservation efforts may be facilitated by an understanding of how present-day population structure has been shaped by historical demographic changes. To investigate the demographic history of porpoises in the eastern North Atlantic, variation in the mitochondrial DNA (mtDNA) control region of 115 porpoises was compared among 4 sampling locations (North Sea, France, Portugal, and West Africa). Genetic variation was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). To put the present study in context within the eastern Atlantic, previously published sequence data from Norway (n = 87) and the Black Sea (n = 9) were included. All areas showed substantial geographic structure as indicated by AMOVA and SAMOVA, and there was significant isolation by distance among sampling areas. The haplotype network, mismatch distribution and Fu’s FS test of population equilibrium suggest there has been a relatively recent range expansion into the northernmost area (Norway), probably as a result of re-colonisation into regions previously iced over during Quaternary glaciation events. In all, these results suggest that harbour porpoises within the eastern North Atlantic show geographic structuring as a consequence of limited gene flow along the coast, and their historical biogeography can be interpreted in light of demographic changes that have influenced the evolutionary patterns observed in the mtDNA sequences.