Many states have established special harvest seasons and hunting zones to target overabundant populations of temperate-nesting Canada geese (Branta canadensis) and protect less abundant northern-nesting populations of Canada geese and cackling geese (B. hutchinsii). To meet management needs for spatially and temporally explicit harvest estimates, we utilized established methods of genetic stock identification and standardized harvest sample collections to estimate proportional contributions of cackling (B. h. hutchinsii) and Canada geese (B. c. maxima and B. c. interior) to 5 consecutive annual harvests (1998–2002) in Michigan, USA. Harvest samples (n = 2,272) were analyzed for several seasons at statewide, regional, and local spatial scales. We expanded upon previous studies that used genetic methods to monitor cackling goose and Canada goose harvests by analyzing harvests within regional and local goose management areas. Likelihood ratio tests were also employed to compare harvest composition among spatial and temporal sampling groups. Tests revealed that proportions of giant and interior Canada geese within local harvests varied significantly during the fall in different hunt zones of Michigan and during different time periods. Adaptive management of temperate-nesting and northern-nesting geese would benefit from accurate estimates of harvest composition, as provided by genetic-based methods. Quantification of changes in harvest composition as a function of variation in season opening date and duration, and bag limits can provide valuable insight into goose migratory behavior and population dynamics. Harvest composition estimates may be used to predict impacts of management prescriptions on mortality rates of specific breeding populations.