Microparasites play an important role in the demography, ecology and evolution of Pacific salmonids. As salmon stocks continue to decline and the impacts of global climate change on fish populations become apparent, a greater understanding of microparasites in wild salmon populations is warranted. We used high-throughput, quantitative PCR (HT-qRT-PCR) to rapidly screen 82 adult Chinook salmon from five geographically or genetically distinct groups (mostly returning to tributaries of the Fraser River) for 45 microparasite taxa. We detected 20 microparasite species, four of which have not previously been documented in Chinook salmon, and four of which have not been previously detected in any salmonids in the Fraser River. Comparisons of microparasite load to blood plasma variables revealed some positive associations between Flavobacterium psychrophilum, Cryptobia salmositica and Ceratonova shasta and physiological indices suggestive of morbidity. We include a comparison of our findings for each microparasite taxa with previous knowledge of its distribution in British Columbia.