Kyrgyzstan can be represented, geomorphologically-speaking, by a transect between the Fergana lowlands and the Tien Shan highlands and is an outstanding area for the study of paleoclimatic conditions relating to climatic changes. These changes have been crucial for the behaviour of past cultures in this area, especially due to the presence of the Silk Road. A Czech environmental team, covering geology, geomorphology, pedology, paleoecology, archaeobotany, malacology, osteology and many other disciplines, has been following up previous survey fieldwork undertaken in this area. Since 2021, the expeditions in the south-eastern Kyrgyzstan (Osh Region) have been aiming at the structure and settlement pattern development in the contact zone between the fertile Fergana basin and the steppe environment at the foothills of the Pamir-Alai and Tian-Shan Mountains, from prehistory until the present, including the material testimony of life on the ancient and medieval Silk Road. This work is a part of an agreement between the University of West Bohemia in Pilsen, the Osh State University and the Institute of History, Archaeology and Ethnology named after B. Dzamgyrchinov of the National Academy of Sciences of the Kyrgyz Republic. One of the major challenges of the ongoing geoarchaeological and palaeoecological research is to link climate changes and changes forced by human action with the transformation of settlement and landscape patterns.