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Between 2002 and 2011, Buller’s albatrosses (Thalassarche bulleri bulleri and T. b. platei) accounted for 34% of albatross interactions in New Zealand trawl fisheries. However, the relative impact of commercial fisheries on each taxon is uncertain as identifying individuals by morphology is challenging. The aim of this research was to develop a genetic identification method for the 2 taxa. To this end, DNA was isolated from blood samples collected from a total of 73 birds breeding at northern Buller’s albatross colonies on the islets of Motuhara and Rangitatahi (total n = 26) and southern Buller’s albatross colonies located on Solander Island and North East Island (total n = 47). The degree of genetic differentiation between northern and southern Buller’s was estimated by using DNA sequences from a 221 bp segment of the mitochondrial Control Region. The genetic structure between northern and southern groups was high (pairwise ΦST = 0.621, P < 0.001). A Bayesian assignment method was used to determine provenance of individuals randomly sampled from fisheries bycatch (n = 97). All bycatch individuals were assigned with maximum probability to either the northern (n = 19) or southern taxon (n = 78; P = 1.00). This study demonstrated that sequences from the mitochondrial control region could reliably be used to assign individuals to either northern, or southern breeding populations, and can be used for determining the provenance of seabird bycatch.