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Hutton’s shearwater (Puffinus huttoni) currently breeds only in 2 colonies in the Seaward Kaikoura mountains, South Island, New Zealand. Conservation measures now include re-locating young to establish a new low altitude colony. To assess the genetic similarity of birds breeding in the 2 colonies as a basis for decisions on sourcing recruits to the present and potentially other new colonies, we genotyped 9 microsatellite loci, with 3-13 alleles, in 30 birds from the Kowhai River catchment colony and 29 from Shearwater Stream. There was no significant population genetic differentiation between the 2 sampling locations. Our results suggest that there would be little genetic risk to mixing birds from both relict colonies in newly established colonies. Future analyses of the former distributions of Hutton’s shearwater, the fluttering shearwater (P. gavia), and the extinct Scarlett’s shearwater (P. spelaeus) will require an analysis of the levels of genetic similarity between birds from the relict colonies and those of former, widely separated colonies.