Many animals move among habitats, and even small-scale dispersal of individuals between habitat patches may have strong implications for population dynamics and structure. Here, we use long-term mark–recapture data combined with extensive genotyping and parentage assignment to investigate the importance of small-scale location change of resident brown trout ( Salmo trutta ) in a small stream (1500 m). During the first summer, juvenile fish dispersed downstream (mean displacement 200 m), with smaller juveniles dispersing longer distances. Downstream movement was also predominant during the first winter, but older fish moved little. This limited dispersal resulted in a significant isolation-by-distance structure for ages 1 and 2, but not for older age groups or for the mature fish. Individual pairwise relatedness coefficients decreased with waterway distance for mature fish during the 2002 and 2003 spawning seasons, but only weakly. Overall, between-site genetic differentiation was stronger for the younger age classes, and the signal decayed with age, indicating that the genetic structure observed in the stream is mainly driven by spatial aggregation of close relatives.