We developed a network of tree-ring width chronologies of larch (Larix sibirica Led.) from upper tree-lines of the southeast Altai Mountains, South Siberia. Annual tree-ring variability of chronologies since A.D. 1710 was compared using factor analysis. The factor analysis clustered eight tree-ring chronologies into two groups that were used for compositing chronologies. One resulting composite chronology (A.D. 1582–1994) averaged sites from upper tree-lines in glacier-free areas and another chronology (A.D. 1090–1999) captured the sites at upper tree-lines in valleys of the Korumdu, Aktru, Yan-Karasu and Kizil-Tash Glaciers (North-Chuya Range). There is no significant difference in the estimated strength of temperature signals (June and July) of the composite chronologies. However, we observed a remarkable contrast in the decadal variability of larch growth between upper tree-lines of glacier-free areas and glacier valleys. The tree-ring growth of larch was coherent among the chronologies for the period A.D. 1582–1725. Suddenly, low-frequency similarity declined around A.D. 1730. The magnitude of differences became more pronounced after A.D. 1775 indicating three periods with opposite growth tendency (1775–18501775–1900–1915 and 1960–1994) that alternated with short periods of coherent growth. We assume that the low-frequency signal in the glacier valley larch chronology accommodates oscillations of both summer temperature and glacier dynamics. The periods of low-frequency departures are consistent with the 19th Century advance and tremendous 20th Century retreat of the glaciers. We argue that expanded glaciers enhance harmful impacts of katabatic wind on larch growth. It appears that employing tree rings from upper tree-lines of glaciated areas for estimation of decadal and centennial variability climatic proxies should be selected with great caution.