In the Elwha River, two hydroelectric dams constructed nearly a century ago fragment previously continuous habitat and isolate migratory bull trout. Removal of the dams is scheduled to begin in 2011, and represents an opportunity to help recover this threatened species. Large-scale disturbance is expected when accumulated sediments behind the dams are released downstream, which may initially negatively affect bull trout. To inform restoration planning, we investigated levels of genetic variation within and among bull trout populations from six Olympic Peninsula watersheds with an emphasis on the Elwha River. We determined genetic relationships among Elwha bull trout from four distinct river sections and performed population assignments for fish collected from the lower Elwha and Dungeness rivers. There were greater levels of variation and gene flow in coastal watersheds (Hoh, South Fork Hoh, Kalaloch) compared to populations isolated by dams (Elwha, North Fork Skokomish). Elwha bull trout represented an independent spawning population and were highly differentiated from other populations. Bull trout from the Elwha (n = 21) and Dungeness (n = 18) estuaries all assigned to the river they there were collected from. Despite long-term fragmentation, there was no significant genetic variation among Elwha bull trout separated by the dams, although fish from the Elwha headwaters were genetically distinct. Results suggest that bull trout still migrate downstream through both Elwha River dams and that anadromous bull trout will likely help to recolonize the Elwha River following dam removal. Baseline data from this study will be useful for monitoring bull trout recovery following dam removal.