High sensitivity methods for detection of bacterial ulcerous syndrome of Coregonus migratorius were approved. Microorganisms of phyla Cytophaga-Flavobacteria, genus Aeromonas, as well as parasitic fungus Saprolegnia ferax were detected in extinctive ulcerous erosion of skin of C. migratorius. We proposed that the most important ecological factors those determined epizootic situation in population of C. migratorius were: fish physiology after long subglacial condition with low feeding intensity, water temperature, and high density of fish during growing period. Microbiological and parasitological monitoring as a part of control of healthiness of the main important hydrobionts of Lake Baikal was proposed.