River valleys in the Tien Shan Mountains of Kyrgyzstan have served as corridors for human dispersal since the Palaeolithic but little information exists on the history of human occupation in this remote and inaccessible region. Here, we report the results of a multidisciplinary study of Airgyrzhal-2, a high elevation (2005 m) site in the Naryn valley in central Kyrgyzstan. Two main occupation horizons were recognized, the earliest belonging to the Mesolithic (12th millennium cal. BC) and a later one dating from the Bronze Age (first half of the 2nd millennium cal. BC). Land snail analyses from the two horizons yielded almost identical assemblages of species of dry, open environments. Archaeobotanical data, however, revealed marked differences. The greater representation of willow/poplar (Salix/Populus) in the charcoal from the Mesolithic suggests more focused activity along the river, which might have been closer to the site at this time. The occurrence of spruce (Picea) and other species in the Bronze Age charcoal indicates exploitation of resources from more distant upland locations. The occurrence of the remains of cereals, including both grains and chaff, provides unexpected evidence for both consumption and cultivation of wheat and barley at this high elevation during the Bronze Age.