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Histrionicus histrionicus (Harlequin Ducks) that winter along the east coast of North America are listed as a population of special concern in Canada, and they use several coastal wintering sites in southern New England that are subject to varying degrees of urbanization. We studied patterns of habitat use by Harlequin Ducks at 12 known wintering sites in southern New England. An average of 327 ± 114 Harlequin Ducks were found at the sites during the winters of 2001–2003. More Harlequin Ducks wintered at sites south of Cape Cod, MA that had greater mollusk (709,133 ± 504,568 versus 97,154 ± 72,427 kcal ha−1) and crustacean (27,907 ± 16,312 versus 1412 ± 1675 kcal ha−1) prey energy density, and a higher index of hunting activity (2.4 ± 1.2 versus 1.4 ± 0.5) than sites to the north. We used logistic regression analysis at 12 sites inhabited by Harlequin Ducks and 12 nearby sites of similar geomorphology that did not support Harlequin Ducks to identify habitat characteristics that best explained their distribution in southern New England. Our analysis identified two habitat characteristics that affected the likelihood a site was used by Harlequin Ducks: 1) the proportion of residential, commercial, and industrial land use within a 100-m radius of the perimeter of the site; and 2) distance to the nearest Harlequin Duck wintering site. However, other factors, including those related to their extremely low population size, need to also be considered as recommendations are developed for the conservation of east coast Harlequin Ducks.