This study summarizes lithological character, C-14 radicarbon age dating and diatom analysis on a 57 cm long gravity core(GC-2-2) from a deep, central part of Lake Hovsgol. GC-2-2 core sediments are lithologically divided into two units: a diatom-bearing Upper Unit (Holocene) and a calcareous Lower Unit (Pleistocene). Diatoms are abundant in the Upper Unit, but are absent in the Lower Unit, except scattered ones in the uppermost part of the Lower Unit. A total of 19 genus and 27 species have been recognized. The majority of diatoms are freshwater planktonic species. The predominant taxa is Cyclotella ocellata (more than 70%), in combination with Cyclostephanos dubius, Stephanodiscus rotula, Stephanodiscus hantzschii, Cyclotella kuetzingana var. schumannii, and Cyclotella radiosa. The absence of diatoms in the Lower Unit is due to low temperature (continuous ice cover formation all year round) and higher salinity in a closed lake system during the Pleistocene. Diatoms begin to appear in the uppermost part of the Lower Unit (11 similar to 13 cm interval) suggesting that the ecosystem of Lake Hovsgol has recovered since the Bolling-Allerod warming. The abrupt increase of diatoms in the 11 cm interval indicates that Lake Hovgol transferred into a fully open lake at the beginning of the Holocene. Diatom assemblage in Lake Hovsgol is characterized by low diversity and low degree of endemism. Low diversity is often in ancient, large lake systems, due to physicochemical homogeneity in the pelagic zone. The lower degree of endemism is indicative of complete collapse of the ecosystem of Lake Hovsgol and the resultant extinction of all diatoms during the Pleistocene. Based on ecological characteristics of some diatom species, the trophic state of Lake Hovsgol during the early Holocene is thought to have been ultraoligotrophic to oligotrophic.