This article is devoted to the analyses of faunal remains found at multilayered habitation site Sagan-Zaba II, which is located on the western shore of Lake Baikal in Eastern Siberia. Zooarchaeolgical studies were conducted on the faunal sample of over 74 000 specimens received during the excavation at this habitation site in 2007–2008. Methods of analysis are focused on determination of taxonomic diversity and include species identification, quantitative assessment, and taxonomic density. Examination of animal remains from the multilayered habitation site Sagan-Zaba II showed that this location started to be used by ancient populations during the Early Holocene. However, Middle Holocene deposits contained the highest numbers for taxonomic abundance in terms of both identified taxa and its quantities. This situation changed during the Late Holocene when animal taxa and its numbers are represented by lesser variability and lower absolute numbers. Based on the identified species, throughout the Holocene Sagan-Zaba II populations were hunting seals, ungulates and other mammals, but also procured a few birds and did some fishing. The earliest evidence of possible domesticated animals is associated with the archaeological materials from layer III lower, which has a wide chronological span 4440–2000 cal. BP, but remains of these animals are most abundant in later Late Holocene layers, especially those dating 1230–940 cal. BP.