Background: In seabirds, the extent of population genetic and phylogeographic structure varies extensively amongspecies. Genetic structure is lacking in some species, but present in others despite the absence of obvious physicalbarriers (landmarks), suggesting that other mechanisms restrict gene flow. It has been proposed that the extent ofgenetic structure in seabirds is best explained by relative overlap in non-breeding distributions of birds fromdifferent populations. We used results from the analysis of microsatellite DNA variation and geolocation (tracking)data to test this hypothesis. We studied three small (130–200 g), very abundant, zooplanktivorous petrels(Procellariiformes, Aves), each sampled at two breeding populations that were widely separated (Atlantic and IndianOcean sectors of the Southern Ocean) but differed in the degree of overlap in non-breeding distributions; thewintering areas of the two Antarctic prion (Pachyptila desolata) populations are separated by over 5000 km,whereas those of the blue petrels (Halobaena caerulea) and thin-billed prions (P. belcheri) show considerableoverlap. Therefore, we expected the breeding populations of blue petrels and thin-billed prions to show highconnectivity despite their geographical distance, and those of Antarctic prions to be genetically differentiated.Results: Microsatellite (at 18 loci) and cytochrome b sequence data suggested a lack of genetic structure in all threespecies. We thus found no relationship between genetic and spatial structure (relative overlap in non-breedingdistributions) in these pelagic seabirds.Conclusions: In line with other Southern Ocean taxa, geographic distance did not lead to genetic differences betweenwidely spaced populations of Southern Ocean petrel species.