The phytoplankton community structures in Ningwu subalpine lakes have been studied and 291 taxa, belonging to 8 divisions, 45 families and 108 genera, have been identified. The species numbers of each sampling station are quite different. The most abundant species are occurred in Lake Mayinghai, and the least in Lake Ganhai. Bacillariophyta, Chlorophyta and Cyanophyta dominate the area, in addition, dominant families, dominant genera and dominant species are also relatively clear. There are 8 dominant species and they are Aphanocapsa elachista, Microcystis aeruginosa, Phormidium tenue, Cyclotella kuetzingii, Fragilaria ulna, Synedra acus, Ankistrodesmus angustus and Chlorella vulgaris. The average phytoplankton cell density is 3.49×10⁶ cells/L in the lakes. The cell density in 0.5 m depth was higher than that on the surface. The initially assessment by four biodiversity indexes is that the water quality in Ningwu subalpine lakes is light-polluted.