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Auckland Island snipe (Coenocorypha aucklandica aucklandica) are presumed to have occurred throughout the Auckland Island archipelago but became restricted to a subset of the islands following mammal introductions. Snipe were known to have survived on Adams Island, Ewing Island, and Disappointment Island. However, it is uncertain whether snipe were continually present on Enderby Island and/or adjacent Rose Island. These islands lie near Ewing Island, and both hosted a suite of introduced mammals until the last species were eradicated in 1993. Using SNPs generated by ddRAD-Seq we identified four genetically distinct groups of snipe that correspond to the expected three refugia, plus a fourth comprised of Enderby Island and Rose Island. Each genetic group also exhibited private microsatellite alleles. We suggest that snipe survived in situ on Rose and/or Enderby Island in the presence of mammals, and discuss the conservation implications of our findings.