We conducted genetic analyses of Aleutian Canada Geese (Branta canadensis leucopareia) from Buldir Island in the western Aleutians and the Semidi Islands in the eastern portion of their breeding range. We compared data from seven microsatellite DNA loci and 143 base pairs of the control region of mitochondrial DNA from the two populations of Aleutian Canada Geese and another small-bodied subspecies, the Cackling Canada Goose (B. c. minima) which nests in western Alaska. The widely separated island-nesting Aleutian geese were genetically more closely related to each other than to mainland-nesting small-bodied geese. The populations of Aleutian geese were genetically differentiated from one another in terms of mitochondrial DNA haplotype and microsatellite allele frequencies, suggesting limited contemporary gene flow and/or major shifts in gene frequency through genetic drift. The degree of population genetic differentiation suggests that Aleutian Canada Goose populations could be considered separate management units. There was some evidence of population bottlenecks, although we found no significant genetic evidence of non-random mating or inbreeding.