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High-altitude lakes, which are very sensitive ecosystems and respond rapidly to climatic changes, are one of the best targets for palaeolimnological studies. Here, we present the record of environmental changes over the last millennium that are recorded in the sediments of El Sol, a tropical, high-altitude, volcanic crater lake on the Nevado de Toluca, Central Mexico. Palaeolimnological reconstructions are based on subfossil Cladocera, diatoms, magnetic susceptibility and chemical analysis of the sediments. In general, Cladocera occurring in tropical regions, and especially at high altitude, have been studied very little. Our data indicate that in the sequence studied, the species diversity of subfossil Cladocera is very low. Only four species were recorded, and the assemblage is dominated by littoral species. Two Cladocera taxa, Alona manueli and Ilyocryptus , found at Lake El Sol are endemic. Cladocera, diatoms and the sediment chemistry show changes in Lake El Sol which are mostly related to climate. The most pronounced climatic signal was obtained for the early Little Ice Age (1350–1625 AD). This cold episode was expressed by a reduction in the frequency of zooplankton (individuals/cm 2 /yr) and diatoms (valves/g of dry sediment) and by changes in the organic carbon content in the sediment. Our results show that human activity was very limited throughout the study period. According to historical data the presence of humans at the lake shore was mostly occasional, usually for ceremonial and ritual purposes, and humans did not have an important influence on the lake ecosystem. Only one period was identified when human activity was important. This period corresponds to the introduction of fish into the lake at the beginning of the 20th century.