Taxonomic composition and structure of microbial communities of Baikalian endemic sponges sampled during mass mortality of these animals were identified using high-performance sequencing. In bacterial community of L. baicalensis 23 phyla were determined, in B. intermedia – 19 ones, phyla of Cyanobacteria, Proteobacteria, Actinobacteria, Verrucomicrobiawere major ones. The studied communities were dominated by phylotypes of chloroplast genes of algae, of cyanobacteria forming films on sponges’ surface, of purple, chemoorganoheterotrophic, methanotrophic, sulphate- and nitrate-reducing bacteria. Composition and structure of major and minor phyla and of dominant phylotypes in microbiomes of sick sponges considerably differed from ones in healthy animals.