Human and non-human faunal bone from the Neolithic and Early Bronze Age periods of Cis-Baikal were analysed for stable isotopes of carbon and nitrogen in order to study regional and temporal variation in diet and subsistence. Both prehistoric and modern faunal species were analysed with all fish from the modern context. Results indicate that regional variation is greater than temporal variation and can be attributed to proximity to Lake Baikal and its rich aquatic resources. Stable isotope analyses of fish and seals from Lake Baikal indicate a wide range of variation in isotope values. δ15N values for the freshwater seals of Lake Baikal average 14 ± 1·1 per mil. Freshwater fish are highly variable in the δ13C values ranging from − 24·6 per mil for the pelagic omul (Coregonus autumnalis migratorius) to − 12·9 per mil for littoral species such as ide (Leuciscus idus). Terrestrial herbivores have much lower δ15N values, ranging from 4 to 5 per mil for deer and elk. These data demonstrate that even in temperate, inland regions, there is sufficient variation in stable isotope values of various food resources to provide useful information about variation in human palaeodiet.