The selective and environmental effects of captivity on several fitness-correlated traits were assessed in smolts of endangered Atlantic salmon, Salmo salar L., from the inner Bay of Fundy, produced via artificial spawning and released into the wild as juveniles. Smolts were sampled as they migrated downstream and identified through microsatellite-based parentage analysis as offspring of either wild-spawning adults or adults that were spawned in captivity. Overall, captive-origin smolts exhibited a significantly later run timing and smaller body size than wild smolts. Significant differences in run timing and body size were also found between captive-origin smolts that had experienced rearing environments that differed in duration of captivity and thermal regime. Significant differences in run timing, fork length and weight were found between first and second generation captive-origin smolts, although the expression of these differences depended on the rearing environment experienced, suggesting a possible genotype by environment effect. The ratio of effective-to-census number of breeders that produced the captive-origin smolts was higher than that of the wild-origin smolts due to successful captive breeding management practices. These results have direct implications for captive breeding and rearing programmes for salmonids and wider implications for understanding the rates of evolutionary and environmentally induced change that can occur in captivity.