Artificial breeding programmes commonly lead to domestication, which is associated with many behavioural differences that can reduce the success of animals released into natural environments. To better understand the factors contributing to domestication, we used a captive population of Chinook salmon (Oncorhynchus tshawytscha) to partition hormonal and behavioural differences to effects of the breeding method and rearing environment. We compared 9-mo-old juveniles from three lines that shared a common genetic background: (1) the Channel line produced by natural spawning and reared in a low-density environment with a natural substrate for approx. 6 mo before being transferred to the hatchery; (2) the Hatchery line produced by artificial spawning; and (3) the Transfer line produced by natural spawning but reared in the hatchery from the eyed-egg stage. Plasma concentrations of 11-ketotestosterone (11-KT) and cortisol were measured in groups of 150 fish and again after 4 d of social interactions in groups of six fish. There was no difference in 11-KT among lines in large groups, but in small groups, Transfer fish had lower 11-KT concentrations and were significantly less aggressive than both Channel and Hatchery fish. Regardless of group size, concentrations of the stress hormone cortisol were nearly twofold higher in Channel fish than in Hatchery and Transfer fish. Furthermore, the elevated cortisol concentrations in Channel fish were associated with 35% lower feeding rates than in the other two lines. Our study details complex behavioural and hormonal responses to breeding method and rearing environment in juvenile salmon.