We investigated crustacean zooplankton communities and their relationships to environmental factors in 13 lakes of Yunnan-Guizhou plateau to determine whether there is a consistent relationship between trophic indicators and crustacean zooplankton biomass or size structure. The lakes showed a wide range of trophic status, with total phosphorus (TP) ranging from 0.013 to 0.268 mg.L−1, and chlorophyll a from 0.9 to 76.26 μg.L−1. Continuous stocking with exotic planktivorous fish had taken place on a wide scale in these plateau lakes. About 36 species of Crustacea were found, of which Cladocera were represented by 20 taxa (12 genera), and Copepoda by 16 taxa (13 genera). Canonical correspondence analysis partitioned these species into two clusters. Physicochemical features and food-webs of different lakes seemed to be the key factors determining zooplankton species composition and distribution patterns. Between the 13 lakes, there was no significant relationship between cladocerans and chlorophyll a suggesting phytoplankton biomass was little controlled by macrozooplankton. The positive correlation between chlorophyll a and copepods suggested the high copepods biomass or size structure caused by the invasion of exotic planktivorous fish had a negative effect on water quality.