We compared genetic characteristics of four aggregations of molting birds (referred to as populations) captured within two regions. Because band resightings and radio telemetry data indicate Harlequin Ducks almost always winter at or near their molting sites we considered these molting aggregates to represent discrete winter populations. Molting Harlequin Ducks were captured at each of the eight sampling sites during July to Sept of 1995, 1996 and 1997 by herding the flightless birds into pens. The sex of each duck was determined by plumage characteristics and aged by bursal probing. Blood was extracted from the jugular or tarsal vein and preserved with lysis buffer. DNA was extracted using Puregene DNA extraction kits.