Epitheliocystis is a condition that has been recognised in a wide range of freshwater and marine fish species. The infection is characterized by intracytoplasmic inclusions in gills and less commonly, skin. Since 2004, molecular evidence has shown that epitheliocystis is associated with Chlamydia-like organisms. Lake trout (Salvelinus namaycush) are raised for release by the Ontario Ministry of Natural Resources at Blue Jay Creek, Manitoulin Island, ON. This facility has experienced yearly epizootics of epitheliocystis during winter. Affected lake trout have marked gill lesions including: severe branchial epithelial cell necrosis, epithelial hyperplasia with thickening and blunting of lamellae and occasionally small to large numbers of scattered epithelial cells containing 10-30 μm bacterial inclusions. The use of PCR primers previously described to identify chlamydia-like organisms has not produced consistent results with the gills of these LT with prominent intraepithelial microcolonies. The use of universal bacterial primers to 16S rDNA and laser capture microdissection in this thesis provide evidence that a novel β-proteobacteria is more consistently associated with affected gills of LT and that this organism may play an important role in these epizootics of EP. NSERC, OMNR, OMAFRA,CONICYT (Chilean Scholarship fund)