Past research has greatly improved our understanding of palaeoenvironmental changes in the Lake Baikal Region, but at the same time has indicated intra-regional variations in this vast study area. Here we present a new AMS-dated late glacial–middle Holocene (ca. 13,500–4000 cal. yr BP) pollen record from Lake Ochaul (54°14′N, 106°28′E; altitude 641 m a.s.l.) situated in the less-studied area of Cis-Baikal and compare reconstructed vegetation and climate dynamics with the published environmental history of Trans-Baikal based on the pollen record from Lake Kotokel (52°47′N, 108°07′E; altitude 458 m a.s.l.). Although both records show comparable major long-term trends in vegetation, there are considerable differences. Around Ochaul the landscape was relatively open during the Younger Dryas stadial, but forest vegetation started to spread at the late glacial/Holocene transition (ca. 11,650 cal. yr BP), thus ca. 1000 years earlier than around Kotokel. While in both regions taiga forests spread during the early and middle Holocene, the marked increase in Scots pine pollen in the Kotokel record after ca. 6800 cal. yr BP is not seen in that from Ochaul, where birch and coniferous taxa, such as Siberian pine, larch, spruce and fir, dominate, indicating different environmental conditions and driving forces in both study regions. However, the pollen data from Ochaul emphasizes that the Cis-Baikal area also saw a continuous increase in forest cover and in the proportion of conifers over birch trees and shrubs during the early–middle Holocene, which may have contributed to a decrease in the number of large herbivores, the main food resource of the Early Neolithic hunter-gatherer groups. This and rather abrupt reorganization of atmospheric circulation, which affected atmospheric precipitation distribution resulting in thicker and longer-lasting snow cover, may have led to a collapse of Early Neolithic Kitoi populations ca. 6660 cal. yr BP followed by a cultural “hiatus” in the archaeological records during the Middle Neolithic phase (ca. 6660–6060 cal. yr BP). The results stress the importance of sub-regional palaeoenvironmental studies and the need for a representative network of well-dated, high-resolution sediment archives for a better understanding of environmental changes and their potential impacts on the hunter-gatherer populations in the archaeologically-defined micro-regions.