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For the lack of historical water ecology monitoring data and the limitations of traditional morphology-based water ecology reconstruction methods, the response mechanism of lake phytoplankton to climate change in the Tibetan Plateau remains unclear. In this study, we reconstructed the succession of phytoplankton community in Lake Gyaring, located in the northeastern Tibetan Plateau, since the 6th century by using sediment DNA metabarcoding. We found that the diversity and structure succession stages of phytoplankton community were consistent with the global temperature oscillation events, namely, the Medieval Warm Period (800–1300 CE). Little Ice Age (1300–1850 CE) and Current Warm Period (1850–2000 CE). The community structure dominated by Chlorophyta in the Medieval Warm Period gradually changed to that dominated by Bacillariophyta in the Little Ice Age. However, the Current Warm Period did not observe the dominant community structure of Chlorophyta similar to that of the Medieval Warm Period. This finding may be due to the climate change of the Current Warm Period was influenced by multiple human activities, such as increased anthropogenic aerosols, which promoted obvious weakening of the intensity of the summer monsoon, leading to decreased soil erosion and lake mixing, and thus may trigger a strikingly different aquatic ecosystem compared to that during the Medieval Warm Period. In this paper, the combination of genomics and palaeollimnology is helpful to explore the response mechanism of phytoplankton to climate change. [Display omitted] [ABSTRACT FROM AUTHOR]