In migratory birds, population-genetic structure is generally low, but philopatric species can have fine-scale patterns of differentiation. We investigated the population-genetic structure of the Canada Goose (Branta canadensis) across multiple spatial scales to determine whether genetic data support current delineations of subspecies and populations for management. We collected samples from two subspecies (B. c. interior and B. c.maxima) and four management populations across Ontario and Quebec. Using 7 microsatellites and 442 base pairs of mtDNA we found that genetic structure varied with scale. F_ST revealed low levels of genetic differentiation between subspecies and management populations, and individual-based clustering revealed no genetic differentiation. However, fine-scale spatial autocorrelation revealed significant levels of relatedness at distances <85 km. The lack of clear genetic structure may reflect recent human management. That our fine-scale analysis revealed significant genetic relationships suggests that genetic structure may increase and in time reflect that revealed by banding data. As our markers were unable to accurately distinguish between subspecies they will be of little use in estimating subspecific contribution to harvested stock. Alternative molecular markers under selective pressure may be more informative in assess targets for harvest.