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The sedimentary diatom records of three shallow lakes in the Altai Mountains, southern Siberia, were examined to assess the nature and timing of Holocene environmental changes. Few paleoenvironmental records, especially reconstructions not based on pollen, have been reported from this region. The lakes differ in elevation, annual precipitation, and catchment vegetation. Diatom assemblages in all lakes were dominated for the entire period of record by small benthic species of Pseudostaurosira Williams & Round, Staurosira Ehrenberg, and Staurosirella Williams & Round. Planktonic taxa only occur in very low abundances (<5%). The most diverse diatom flora was found in Dzhangyskol, which is situated at the lowest elevation within a forested catchment. A lack of detailed information on the ecological preferences of the dominant taxa and the complexity of environmental drivers make direct interpretation of the diatom record difficult. However, other proxies suggest that dramatic shifts in dominance between Staurosira elliptica and Staurosirella pinnata in Grusha Ozero reflect millennial-scale variability in climate. Together, chironomids and diatoms provide evidence of a cooling possibly correlative to the Younger Dryas Stade and subsequent early-Holocene warming consistent with pollen evidence of afforestation, which also is likely linked to increased humidity. By 6,000 cal year BP, the transition to a cooler, more continental climate had begun. The diatom record of Akkol shows significantly less variation in diatom community composition, but biogenic silica accumulation rates, a proxy for diatom productivity, appear to reflect climatic variability driven by insolation trends over the past 8,000 years. Long-term variability in Dzhangyskol is not clearly linked to climate.