The psbA gene, which encodes a major photosystem II protein (protein II or D1), is a marker for the presence of phototrophic organisms in water communities. We have pioneered the use of this marker for studying the diversity of phototrophic microflora of freshwater invertebrates. The object of the study is the microbial associations accompanying the endemic Baikal sponge Baikalospongia intermedia and the surrounding aquatic microbial community. Analysis of the psbA gene sequences in the examined microbiomes demonstrates the presence of various phototrophic groups, such as Cyanobacteria, Chlorophyta, Heterokonta, Haptophyta, and Ochrophyta algae, as well as cyanophages. A total of 35 unique psbA gene sequences have been distinguished in the microbial communities of the endemic sponge B. intermedia and 32 unique sequences in the water community surrounding the sponge. These data demonstrate the involvement of sponge symbiotic communities in the accumulation of primary production and carbon cycle in the Lake Baikal ecosystem.