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Dams along the Deschutes River (DR) in central Oregon have blocked fish migration for over 40 years. Reestablishment of anadromous fish runs above the dams as part of a fish passage plan may introduce fish pathogens, such as Myxobolus cerebralis, the myxozoan parasite that causes salmonid whirling disease. This parasite is carried by adult salmon that stray into the DR system during their return to enzootic areas of the upper Columbia River basin, and it is now known to be established in at least one lower DR tributary. The life cycle of M. cerebralis involves two obligate hosts: a salmonid and the oligochaete worm Tubifex tubifex. To determine the likelihood of parasite establishment above the DR dams, we conducted benthic sediment surveys between 1999 and 2007 and found that T. tubifex had a patchy distribution and low relative abundance. Mitochondrial 16S ribosomal DNA gene analysis indicated that two lineages of T. tubifex (III and VI) were present both above and below the dams. Laboratory susceptibility studies to characterize differences in infection prevalence and parasite production between nine T. tubifex populations revealed that production varied considerably among exposed groups and was proportional to the number of lineage III worms present. Our results suggest that M. cerebralis could become established above the dams if infected fish are allowed passage into the upper DR system, but not all areas of the DR basin can be classified as having the same likelihood for parasite establishment, and the potential impact will be location dependent.