Twelve dams have been built along the Lianjiang River, the largest tributary of the Beijiang River in Guangdong Province, China. To understand the spatial distribution of zooplankton diversity developing after the establishment of these dams and cascades, and also the effects that these dams have had on zooplankton community structure, a study was conducted on the aquatic ecosystem in October 2007. Twelve sampling sites (S1-S12) along the main stream of Lianjiang River were established to study the composition of different groups of zooplankton and dominant species, the spatial distribution of abundance, biomass, diversity index of zooplankton as well as the zooplankton community, and relationships with environmental factors. Records showed that there were 76 species of zooplankton, which included 19 species of protozoa, 25 species of rotifer, 17 species of cladocera and 15 species of copepoda. Species numbers of zooplankton were greatest in sites S2 to S4, and lowest in S5. The dominant species were Stentor polymorphrus, Brachionus calyciflorus, Bosmina longirostris and Ectocyclops phaleratus, and significant differences in the distribution of dominant species existed between sampling points. Abundance of zooplankton fluctuated between 921.00 and 2,160.35 individuals/L, with highest abundance occurring in S5 and lowest in S1. Biomass of zooplankton fluctuated between 0.198 and 0.699 mg/L, with the highest value occurring in S5 and the lowest in S1. Generally, the values of Margalef species richness index, Shannon-Wiener diversity index and Pielou Evenness index of different zooplankton groups showed higher in upstream and lower in middle and downstream. PCA analysis showed a significant association between zooplankton community and environmental factors such as ammonia nitrogen, permanganate index, pH and transparence. We concluded that significant differences in ecological factors between habitats, such as nutrients, caused by cascade development, were the key factors determining the spatial distribution of zooplankton diversity in the Lianjiang river.