Shy and white-capped albatrosses, Thalassarche cauta and T. steadi, respectively, are phenotypically similar and are known to suffer fisheries-related bycatch mortality across their foraging range. Assessments of the extent or scale of impact of bycatch mortality on these species have previously been precluded by difficulties identifying bycatch carcasses to species level. In this study, a fast and simple molecular test based on a single nucleotide polymorphism in mtDNA of shy and white-capped albatrosses was used to determine the species composition of fisheries bycatch carcasses recovered from Australian, New Zealand, and South African waters. The only area where bycatch mortality of both species co-occurred was in Tasmanian waters; in all other zones the bycatch was exclusively comprised of white-capped albatrosses. Genotypic provenance assignment tests of shy albatrosses, a species with significant genetic structure between island colonies, correctly assigned 72% to their island of origin. These data are the first to provide insight into the relative vulnerability of shy and white-capped albatrosses to bycatch mortality across their foraging range, and to establish the vast differences in the at-sea distributions of these two species.