Stocking of hatchery-raised Chinook salmon has been the principal tool utilized by fishery managers for controlling alewives in Lake Ontario and elsewhere in the Great Lakes. Stocked Chinook salmon are also often viewed by anglers as the principal source of maintaining catch rates. Stocking levels are often controversial and set with limited information about the relative contribution of wild fish to lake-wide populations. Recent research documenting large numbers of age-0 fish in tributaries suggested that wild reproduction was increasing and greater than previously thought. Estimating the contribution of wild Chinook salmon is imperative for successful management of this economically important recreational fishery. To differentiate wild from hatchery-derived Chinook salmon, we developed and validated a classification rule from scale pattern analysis of known-origin fish that was based on the area of the scale focus and the distance between the scale focus and the first circulus. We used this technique to determine the annual proportion of anglercaught, age-3 wild Chinook salmon in Lake Ontario from 1992 to 2005. On average over 14 years, the annual proportion of wild age-3 Chinook salmon was 62% (±13.6%, 95% CI), but has varied between 24% (±9.4%) and 82% (±11.2%). Wild fish have been a high proportion of the Chinook salmon population in Lake Ontario since the late 1980s throughout a period when the lake underwent considerable changes, suggesting that wild and hatchery-origin Chinook salmon are both important components for managing the predator-prey dynamics in Lake Ontario and maintaining angler catch rates.