We used six polymorphic microsatellite loci to analyze the population genetic structure of bull trout Salvelinus confluentus in the Boise River, Idaho, and we compared our results with previous data from similarly sized river systems in western North America. Within the Boise River, we found low genetic variation within and significant differentiation among sample sites. Two cohesive groups of populations were associated with the two major subbasins in this system, which we attributed to long-term reduction of gene flow or distinct sources of colonization at this scale. We observed a significant pattern of isolation by distance in one subbasin and not in the other; this result suggests that the relative influences of gene flow and drift have differed between the two subbasins. Ecologically defined patches of suitable habitat were not good predictors of genetic variation among samples. Dams and other anthropogenic barriers have recently changed the potential for gene flow and genetic drift but were not associated with the major boundaries of genetic differentiation. There was some evidence of lost genetic variation in smaller patches that were physically isolated by both natural and anthropogenic barriers. We found a large range of within-population genetic variation and among-population genetic differentiation for bull trout from river basins across the species' range, but our estimates in the Boise River were the lowest (or among the lowest) observed. The relative roles of drift and gene flow appear to vary strongly at both fine and broad spatial scales. We cannot presume that the physical and ecological processes influencing the genetic population structure of bull trout in one region will accurately reflect those in another region; this may have important implications for conservation and management actions.