Abstract: Shallow lakes, sensitive to environmental changes due to low environmental carrying capacity, generally experience decreases in ecosystem function and even regime shifts after over-exploitation. Surface sediments of 18 shallow lakes in Yunnan were collected and analyzed to identify the spatial pattern and the influencing factors of cladoceran communities. The results showed that there was significant heterogeneity in the spatial distribution of cladocera in those lakes. For example, the cladoceran community was generally dominated by benthic taxa in alpine lakes, while there was a clear replacement of benthic cladocerans by planktonic ones with increasing nutrient levels across lakes from Southeast Yunnan. Altitude and total phosphorus were the main driving factors, which independently explained 22.0% and 7.7% of the change in cladocera communities, respectively. The altitude gradient and related changes in climate and catchment features were the main factors in structuring cladocerans for shallow lakes of Yunnan, while the anthropogenic impacts on cladoceran distribution was significant via the processes such as catchment development, pollutant input and macrophyte changes. Meanwhile, the interaction between elevation and total phosphorus explained 26.3% of the total variance in cladoceran community shift, indicating that the increase in human activity intensity in lakes at lower altitudes would have stronger impact on cladocerans through anthropogenic nutrient inputs.