Prions (Pachyptila) are small seabirds with a Southern Hemisphere breeding distribution. Antarctic prion (Pachyptila desolata) and Salvin’s prion (P. salvini) are two species that are regularly recorded in New Zealand as beach-wrecks but they are difficult to distinguish morphologically. Salvin’s prion is restricted to breeding on the Prince Edward Islands and Crozet Islands in the Indian Ocean but Antarctic prions have a circumpolar breeding distribution on numerous sub-Antarctic and Antarctic islands in the Southern, South Atlantic and Indian Oceans. Our aim was to examine the level of mitochondrial DNA (mtDNA) structuring within Antarctic prion and Salvin’s prion colonies, to test whether this technique can determine the provenance of beach-cast birds. The Auckland Islands Antarctic prion population exhibited distinct mtDNA haplotypes from all other populations, supporting the suggestion that these islands may have been an ice-free refugium during the Last Glacial Maximum. All other sampled breeding populations shared haplotypes, limiting the use of these sequences for determining the provenance of beach-cast birds. None of our museum specimens of Salvin’s prion collected from breeding colonies produced DNA sequences. This result indicates that the method by which these specimens, which were collected in the 1960s and 70s, were preserved, or subsequent treatments, has resulted in the loss of their DNA.