Ichthyophonus hoferi is a parasitic protozoan affecting marine and anadromous fishes, including salmonids (Kocan et al. 2004). Gross clinical signs associated with Ichthyophonus infection are multifocal white lesions on the heart, liver, spleen, and muscle tissue (Fig. 2 A, B). Ichthyophonus is likely an orally transmitted parasite with the potential to be horizontally transferred (Kocan et al. 2010). In the mid 1980’s Ichthyophonus was identified in Chinook salmon (Oncorhynchus tshawytscha) by the Alaska Department of Fish and Game (ADFG) and the U.S. Fish and Wildlife Service, after fishermen noted an increase of white pustules on heart and muscle of harvested Chinook salmon. Fishermen also noted that the flesh did not dry properly and had an unpleasant fruity smell (Kocan et al. 2004). Large scale necrosis in tissues can lead to organ failure, decreased stamina, and pre-spawning mortality (Kocan et al. 2006). Ichthyophonus has caused major reoccurring epizootics and mass die-offs in Atlantic herring, (Clupea harengus), with peaks of disease prevalence in June and November (Kramer-Schadt et al. 2010). Rainbow trout (Oncorhynchus mykiss) infected with Ichthyophonus showed significant reduction in hematocrit pointing to reduced swimming performance (Rand and Cone 1990). In recent years, Chinook salmon stocks of Arctic-Yukon-Kuskokwim region (AYK) have had low abundance and salmon returns did not hold up to pre-season expectations based on escapement in the corresponding brood years (JTC 2011). In response, fisheries managers cancelled or restricted commercial, subsistence, and sport fishing since 2008. These actions harshly impacted U.S. subsistence fisheries along the Yukon River, but succeeded in the interim management escapement goals into Canada as part of the Pacific Salmon Treaty between the U.S. and Canada. Yukon River Chinook salmon are undergoing one of the longest salmon migrations in the world. They must acquire considerable energy reserves before river entry to energetically prepare for this effort. Rahimian (1998) noted an association of ichthyophoniasis with reduced fish body reserves and emaciation thus complicating successful completion of the spawning migration. Okamoto et al. (1987) showed a positive relationship between Ichthyophonus-related mortality and water temperature with 100% mortality occurring at 15°C to 20°C in rainbow trout. Similarly, Kocan et al. (2009) showed significantly reduced swimming performance in Ichthyophonus-infected rainbow trout at 15°C to 20°C. In-river conditions in the Yukon River have changed over the past 30 years, with June water temperatures having increased by approximately 2.5ºC (Horstmann-Dehn unpublished data).