Quantifying the contribution of wild (naturally spawned) and hatchery Chinook salmon (Oncorhynchus tshawytscha) to the mixed-stock ocean fishery is critical to understanding their relative importance to the persistence of salmon stocks. The inability to distinguish hatchery and wild salmon has inhibited the detection of declines or recoveries for many wild populations. By using Chinook salmon of known hatchery and wild origin, we established a baseline for separating these two sources using otolith microstructure. Otoliths of wild salmon contained a distinct exogenous feeding check likely reflecting an abrupt transition in food resources from maternal yolk not experienced by fish reared in hatcheries. Daily growth increments in otoliths from hatchery salmon immediately after the onset of exogenous feeding were wider and more uniform in width than those in wild fish. The discriminant function that we used to distinguish individuals reared in hatcheries or in the wild was robust between years (1999 and 2002), life history stages (juveniles and adults), and geographic regions (California, British Columbia, and Alaska) and classified fish with ~91% accuracy. Results from our mixed-stock model estimated that the contribution of wild fish was 10% ± 6%, indicating hatchery supplementation may be playing a larger role in supporting the central California coastal fishery than previously assumed.