Quantitative diatom abundance and species composition was studied in the longest 81-m Lake Hovsgol drill core, HDP-04. Lake Hovsgol diatom biostratigraphy of the past 1 Ma includes 14 local diatom assemblage zones (LDAZ). Planktonic diatom flora of Lake Hovsgol is dominated by members of Stephanodiscus and Cyclotella. A large-scale shift from Stephanodiscus-dominated to Cyclotella-dominated flora occurred in the mid-Brunhes chron. Significant morphological variability of Cyclotella ocellata complex and Cyclotella cf. minuta, as well as the presence of new extinct endemic taxa of genus Stephanodiscus, suggest long speciation and/or adaptation history of diatom flora. The recognition of taxa morphologically similar to the extinct endemic species of Lake Baikal suggests potential correlation ties between Lake Hovsgol and Lake Baikal diatom biostratigraphies around the MIS 17, MIS 25, and, possibly, MIS 15 interglacial intervals. Narrow peaks of diatom abundance in the Lake Hovsgol sedimentary record are episodic and short-lived. These peaks may represent humid optima of past interglacials and/or interstadials, characterized by elevated surface runoff in the Hovsgol basin and relative highstands of the lake.