Endemic freshwater sponges (Demosponges, Lubomirskiidae) dominate in Lake Baikal and are multicellular filter-feeding animals represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of the L. baicalensis have been an urgent problem of Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria in microbiomes of diseased sponges of the families Flavobacteriaceae and Oxalobacteraceae were dominant. Both species are opportunistic pathogens common for freshwater ecosystems. The aim of our study is to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. The first one attacks the other cells using type VI secretion system, suppress gram-positive bacteria with violacein pigment and regulate its own activity via quorum sensing. It makes the floc and strong biofilm by exopolysaccharide biosynthesis and PEP‐CTERM proteins expression. The second one utilizes the fragments of cell walls produced of polysaccharides. Named two strains have noticeable difference in carbohydrates acquisition. We described the possible way of joint occupation of ecological niche into freshwater sponge microbial community. This study expands understanding about symbiotic relationship of microorganisms with freshwater Baikal sponges.