Absrtact The ecological state of the southern part of Lake Baikal was assessed in 2017 based on the phytoplankton and bacterioplankton structure. Nineteen functional groups were identified, five of which played the main role: Z (picocyanobacteria from oligotrophic lakes), L-O (dinoflagellates and cyanobacteria typical of mesotrophic lakes in summer), X1 (species typical of nutrient-rich shallow lakes), MP (mero- and tycho-planktonic species, mainly diatoms), and E (phytoflagellates typical of oligotrophic lakes). The values of community index Q, obtained on the basis of data on the structure of phytoplankton, indicated the excellent ecological status of the lake. Waters of the southern part of Lake Baikal were characterized as oligotrophic and oligosaprobic, while the waters on sites "Shamansky Cape" and "City of Baikalsk" tended to the mesotrophic and beta-mesosaprobic status according to the data on the chlorophyll a content and microbiological parameters. The absence of significant correlations between phyto- and bacterioplankton parameters may also indicate the oligotrophic status of coastal waters in the southern part of Lake Baikal.