Abstract– Comparing genetic and demographic estimates of dispersal in freshwater fish can improve understanding of movement distributions and population connectivity. Here we examined genetic variation among mottled sculpin (Cottus bairdi) in the Nantahala River (North Carolina, USA) to compare genetic estimates of dispersal with estimates derived from mark–recapture studies of individual movement. Microsatellite-based analysis of gene flow revealed evidence of strong isolation by distance among locations spanning only 5.6 km and limited dispersal among clusters of sites separated by swift cascades. Estimates of between-cluster contemporary dispersal rates derived from Bayesian assignment tests ranged from 1% to 6%, with most movement occurring among adjacent clusters in a downstream direction. Evidence of a long-term net immigration asymmetry and decreasing genetic diversity from downstream to upstream locations indicates that historical patterns of stream colonisation contrast with contemporary dispersal patterns. Our findings are largely consistent with predictions from individual movement patterns but suggest that long moves (>500 m) are more frequent, and maximum dispersal distances are greater than what has been reported from mark–recapture studies. The discrepancy may reflect spatial limitations of mark–recapture methods or temporal variation in dispersal in individuals and populations.