The chrysophyte stomatocyst composition in phytoplankton of Lake Baikal in 2016 was studied using scanning electron microscopy. 20 morphotypes were detected, 8 of which were seen in the lake for the first time, and 5 were described as novel. For 3 morphotypes the species was determined based on the scale presence and structure.

Complex algological and hydrochemical studies were performed in July 2017 at the mouths of Upper Angara and Kichera rivers, as well as three mouths of Angara-Kichera estuary-Dushkachanskoye, Srednee and Dagarskoye, which supply water to Lake Baikal. The species diversity of scaled chrysophytes was studied via scanning and transmission electron microscopy. A total of 31 species and intraspecific taxa were detected: Chrysosphaerella-1; Paraphysomonas-2; Spiniferomonas-8; Mallomonas-14; Synura-6. As a result, the list of scaled chrysophyte species in the Baikal region was extended by 3 taxa and currently includes 76 species and intraspecific taxa, thus making its diversity of scaled chrysophytes the highest in the world.

An estimate of the role of endemic diatom algae of Lake Baikal, their contribution to numerical abundance and to biomass, was obtained on the basis of long-term monitoring in the pelagic zone, and in shallow water bays and near the mouths of rivers. Endemic diatoms are distributed over a major part of the lake, except for shallow-water bays. During a major part of the year, they dominate in biomass and in numerical abundance, making a major contribution to the rate of accumulation of modern sediments.

Heterotrophic protists Rotosphaerida, Thaumatomonadida, and centrohelid heliozoans are among the less studied silicified protists in terms of their biogeography and ecology. These organisms inhabit fresh and brackish water, and leave behind siliceous structural elements after death that are species‐specific and amenable to electron microscopic analysis. This paper is the first to present data on species richness and taxonomic structure of silica‐scaled heterotrophic protists—rotosphaerids, colorless free‐living thaumatomonad flagellates and centrohelid heliozoans—in the large continuous water system of Siberia connecting Lake Baikal to the Kara Sea. In the study area, electron microscopy revealed 21 centrohelid heliozoan species from the genera Raphidiophrys (1), Acanthocystis (7), Choanocystis (3), Raineriophrys (2), Raphidocystis (6), and Pterocystis (2), seven rotosphaerid species from the genera Pinaciophora (3), Turriplaca (2), Rabdiophrys (1), and Pompholyxophrys (1), and one thaumatomonad flagellate species Thaumatomastix. Two species of rotosphaerids, Rabdiophrys cf. anulifera and Pinaciophora tridentata, and two species of centrohelid heliozoans, Acanthocystis cf. tubata, and A. cf. cornuta, were found in the waters of Russia for the first time. The most widespread species in fresh water from Lake Baikal to the Lower Yenissei River were Pinaciophora fluviatilis and Raineriophrys cf. fortesca. These species disappeared from the protist assemblages of the Yenissei gulf of the Kara Sea due to higher salinity, with only three species, Acanthocystis cf. mylnikovi (at 3.12‰ salinity) and A. pectinata and Raphidocystis sp. 2 (at 8‰ salinity), found in the area. The sensitivity of silica‐scaled heterotrophic protists to changes in habitat parameters suggests that these microeukaryotes could be new indicator organisms.