Abstract: In this study, water samples were collected from 13 sections in the Yongjiang River from March 2011 to February 2012. Physical and chemical factors were analyzed according to national standards. The structure characteristic and the seasonal changes of the zooplankton communities were measured by the qualitative and quantitative methods. 95 species in water samples were recorded. Among them, 24 genera and 72 species of Rotifera, 5 genera and 10 species of Cladocera, 11 genera and 13 species of Copepoda, and 4 other categories of invertebrate larvae were identified. The dominant species were Brachionus and Keratella, and the abundances of them in the total zooplankton were 22.1% and 20.2%, respectively. The abundance of zooplankton in each section showed a significant seasonal variation. From Section 1 to 6, the abundance peaks appeared in spring, and from Section 7 to 13, the peaks were presented in summer. The maximum peak of zooplankton abundance appeared in Section 5 (3160 ind./L). The biodiversity indexes of zooplanktonic communities were lower in the upstream sections compared with those of mid-downstream sections. The intermediate disturbance hypothesis was used to explain the results. The two-way ANOSIM analysis and Bray-Curtis similarities on hierarchical clustering analysis were used to analyze the similarities of zooplanktonic communities in the river. The results revealed that there were significant difference among the sections (R=0.264, P=0.1%) and seasons (R=0.234, P=0.1%), and the difference among seasons were more significant than the difference among sections. The maximum seasonal difference of zooplanktonic communities was presented between spring and summer. Principal component analysis (PCA) showed that in different sections the zooplanktonic communities were affected by CODCr mainly, followed by TN, DO and BOD5; when the seasonal changes were considered, the zooplanktonic communities were affected by PH mainly, followed by TN/TP, salinity and temperature.