Samples were carried out at 340 sites of four functional areas in Zhalong Wetland during July and August 2010 in order to study the structure of phytoplankton community and its relationship with environment factors. Totally 6 phylum, 80 genera and 354 species of phytoplankton were identified. The phytoplankton abundance ranged from 0.06×10⁶ to 37.82×10⁶ cells/L. The dominant species were Chlorella vulgaris, Cyclotella meneghiniana and Trachelomonas volvocina. The phytoplankton community structures in different functional regions were different. In the core region, the dominant species were Navicula radiosa, Cocconeis placentula and Rhopalodia gibba, while Oscillatoria princes and Anabaena azotica were dominant species in the discharge region. Principal components analysis indicated that turbidity and total phosphorus in the water environment were main factors effecting the growth of phytoplankton in Zhalong Wetland. Canonical correspondence analysis illuminated total nitrogen, total phosphorus, turbidity and conductivity could be the main forces structuring on the phytoplankton community in Zhalong Wetland. Cymbella cistula, Asterionella formosa, Chlorella vulgaris and Trachelomonas volvocina were affected greatly by physicochemical factors.