Concern about the conservation and management of harbour porpoise (Phocoena phocoena) populations, which have experienced relatively large incidental fishery kills in localised areas throughout their range, has prompted research to better understand their population structure. Both mitochondrial and nuclear (microsatellites) DNA were used to examine the intra-specific structure of harbour porpoise inhabiting the eastern North Pacific Ocean. Null hypotheses of panmixia were tested after mitochondrial DNA (mtDNA) control region sequence data (402 base pairs; n = 249) and allele frequency data (9 polymorphic loci; n = 194) were sub-divided into geographic strata defined a priori. Strata were based on sampling discontinuities and not discontinuities in population distribution. The mtDNA and nuclear gene data revealed statistically significant genetic differentiation between most strata (α = 0.05) suggesting demographic independence of fairly small sub-units within the population. Since harbour porpoises are essentially continuously distributed in the eastern North Pacific, this degree of genetic differentiation was unexpected and needs to be considered in developing a sound management plan to protect them.