The identification and assessment of island endemics is a conservation priority. We genotyped 115 rock ptarmigan from five insular populations in the Aleutian-Commander archipelago and two Alaska mainland populations to identify conservation units, assess genetic diversity and gene flow, and to determine whether populations have declined over time. We found four distinct populations that appear to be completely isolated and which correspond closely to recognized subspecies. The most geographically isolated populations also have the lowest genetic diversity. Three populations (Attu Island, Rat Islands, and Adak Island), which each experienced historic introductions of an exotic predator, showed genetic signals of declines, but the timing did not correspond with the introduction. We recommend management of each endemic group as a unique conservation unit.