Geographical variation in two related seabird species, the razorbill (Alca torda) and common guillemot (Uria aalge), was investigated using sequence analysis of mitochondrial DNA (mtDNA) control regions. We determined the nucleotide sequence of the variable 5′ segment of the control region in razorbills and common guillemots from breeding colonies across the Atlantic Ocean. The ecology and life history characteristics of razorbill and common guillemot are in many respects similar. They are both considered highly philopatric and have largely overlapping distributions in temperate and subarctic regions of the North Atlantic, yet the species were found to differ widely in the extent and spatial distribution of mtDNA variation. Moreover, the differences in genetic differentiation and diversity were in the opposite direction to that expected from a consideration of traditional classifications and current population sizes. Indices of genetic diversity were highest in razorbill and varied among colonies, as did genotype frequencies, suggestive of restrictions to gene flow. The distribution of genetic variation suggests that razorbills originated from a refugial population in the south-western Atlantic Ocean through sequential founder events and subsequent expansion in the east and north. In common guillemots, genetic diversity was low and there was a lack of geographical structure, consistent with a recent population bottleneck, expansion and gene flow. We suggest that the reduced level of genetic diversity and differentiation in the common guillemot is caused by an inherent propensity for repeated population bottlenecks and concomitantly unstable population structure related to their specialized feeding ecology.