Because captivity constitutes a drastic environmental change, domestication is expected to induce a rapid genetic selection for behavioural traits. In this study, we searched for genetic differences in behaviour among brown trout juveniles from two strains differing for their domestication history, i.e. an almost pure native wild Mediterranean population (W) and an Atlantic domesticated strain (D). In order to assess pure genetic differences among strains, males from the two origins were mated with Mediterranean females to produce two experimental crosses (WW and WD). The swimming activity characteristics of individual WW and WD juveniles were compared before and after the application of a stress (light switched off suddenly, followed by a 5-min period of darkness). For each of the fish observed, mating type origin (WW or WD) was unambiguously reassigned by genotyping. Behavioural responses differed between WD and WW fish. Angular velocity and the time spent immobile were greater for WW fish both before and after the short period of darkness, indicating higher reactivity. Once the light had been turned on again, mean velocity and total distance travelled were higher in WD than in WW fish. WD fish tended to recover levels of swimming activity higher than those before the dark period. This study therefore demonstrates an impact of genetic origin and domestication on swimming activity repertoire (higher reactivity in WW fish), a behavioural trait of particular importance for individual ecological performance. Owing to the contrasted domestication history of the two strains used in the comparison, we assume that the domestication level largely contributes to the behavioural changes observed.