The harbour porpoise, Phocoena phocoena, experiences high levels of nonnatural mortality owing to interactions with commercial fisheries throughout its range. To accurately evaluate the significance of this bycatch, information on population structure is required. We have examined the population structure of this species in the northwest Atlantic Ocean using mitochondrial DNA (mtDNA) sequence and nuclear microsatellite data. Samples from four previously proposed summer breeding populations—the Gulf of Maine, eastern Newfoundland, the Gulf of St Lawrence and West Greenland—were analysed. Control-region sequences revealed a significant partitioning of genetic variation among most of these summer populations, indicating that northwest Atlantic harbour porpoises should not be considered one panmictic population. Analysis of females alone yielded the highest levels of population subdivision, suggesting that females are more philopatric than males. At least three management units may be defined for harbour porpoises in the northwest Atlantic based on these data. Analysis of six microsatellite loci failed to detect significant population subdivision. Male-mediated gene flow may maintain homogeneity among nuclear loci, while female philopatry is sufficient to produce a signal of population subdivision in the maternally inherited mtDNA genome. mtDNA analyses also indicate that winter aggregations of harbour porpoises along the US mid-Atlantic states comprise animals from more than one summer breeding population.