Dams fragment aquatic networks and impact the evolutionary dynamics of migratory fish populations. Historically, the Lake Pend Oreille-lower Clark Fork River system in Idaho and Montana supported a large metapopulation of adfluvial westslope cutthroat trout (westslope). These fish matured in the lake and made upstream spawning migrations to their natal tributaries in the river. Currently, dams allow downstream passage for juvenile fish to the lake, but no upstream passage for adults. We examined 19 microsatellite and anonymous nuclear loci to characterize spatial patterns of non-native rainbow trout (rainbow) genetic introgression in westslope populations upstream and downstream of these dams. We detected hybridization at 20 of 42 sites sampled throughout the system, with rainbow introgression ranging from 1.1 to 99.8%. Rainbow introgression was higher in tributaries downstream of both dams (12 of 18 sites downstream vs 6 of 22 sites upstream). Within tributaries, hybrids were more common in lower sections and only one sampled site contained a hybrid swarm. Fish collected below both dams during the spawning migration were admixtures of westslope, rainbows and hybrids with an average rainbow introgression of 48%. Phenotypic criteria reduced rainbow introgression to less than 1% for putative westslope identified for selective upstream transport at both dams. Lack of upstream fish passage at these dams has likely constrained spread of hybridization and increased isolation among non-hybridized westslope populations by reducing the abundance of the migratory life history form in areas upstream of these dams.