We carried out a first study of Lake Baikal epiphyton on six species of submerged macrophytes: Myriophyllum spicatum L., Potamogeton perfoliatus L., Potamogeton sp., Sparganium gramineum Georgi, Ceratophyllum demersum L., and Elodea сanadensis Michaux. We identified 70 epiphyton species and intraspecific taxa belonging to 3 phyla, viz. Ochrophyta, Cyanobacteria, and Chlorophyta. Nine species of Cyanobacteria were new records for Lake Baikal. Epiphyton communities differing in species composition and quantitative characteristics grew on diverse species of submerged macrophytes. High levels of species richness were recorded on Sparganium gramineum and Potamogeton sp., whereas low diversity of epiphyton was observed on Myriophyllum spicatum and Elodea canadensis. A monodominant community was revealed on the invasive Elodea canadensis represented by Cocconeis placentula var. placentula. Specific characteristics of morphology of submerged macrophytes influenced the structural organization and quantitative development of epiphyton. Epiphyton abundance and biomass were higher on upper sections of most plants than on lower sections, probably because of canopy shading of macrophyte lower portions.