Across its range, the Atlantic Puffin Fratercula arctica is divided into four separate genetic clusters that correspond with geography and/or size differences. However, in the Western Atlantic High Arctic, there is a Puffin colony (Thule) that comprises two discrete size phenotypes. Using whole genome sequencing data of six Thule individuals from these two phenotypes, we found that Thule consists of three distinct genetic clusters, with no signs of recent interbreeding. Our results suggest the beginnings of a potential northward shift of boreal Atlantic Puffins in the West Atlantic, consistent with responses to a warming High Arctic climate.