Host biodiversity can impact disease risk and influence the transmission of parasitic disease. Stream sediment dwelling worms, Tubifex tubifex, are the intermediate host of the parasite that causes Whirling disease (WD) in salmonid fishes. The parasite is native to Europe, but has been introduced into at least 25 states since 1950 with large impacts on trout populations in the Western United States. Genetic diversity of T. tubifex is correlated with variation in WD virulence and susceptibility, and two major lineages (I and III) are found in the Madison River, Montana, USA.  We examined spatial and temporal variation in T. tubifex genotypes and rate of infection in 2004 and 2005 at sites in the Madison River with high, low and intermediate fish infection rates. The relative abundance of the lineages varies among sites and lineage III shows higher rates of infection. These results suggest that spatial variation in the worm communities may be correlated with the wide range of infection in natural streams. In addition to providing information on a disease with high ecological and economic importance, the study shows these sediment dwelling worms provides an excellent experimental venue to test hypotheses about biodiversity and parasite transmission.