Abstract: An investigation was conducted on the phytoplankton’s community composition, abundance, and their relations with environmental factors in Beixi of Jiulongjiang River, Fujian Province in February (dry season), May (wet season), and October (normal season), 2011. A total of 107 phytoplankton species were identified, belonging to 64 genera and 7 phyla. The dominant species changed with seasons. Campylomonas marssoni and Cyclotella meneghiniana dominated in dry season, Scenedesmus quadricauda and Crucigenia tetrapedia dominated in wet season, and Merismopedia tenuissima dominated in normal season. The phytoplankton’s abundance was the highest in dry season (averaged 154.77×10⁴ cells·L^-1), followed by in normal season (76.40×10⁴ cells·L^-1), and in wet season (45.40×10⁴ cells·L^-1). The abundance in dry and normal seasons was significantly positively correlated with water ammonium nitrogen concentration (P<0.05), while that in wet season was significantly positively correlated with water temperature (P<0.01). Canonical correspondence analysis (CCA) showed that water temperature was the most important factor affecting the phytoplankton’s community structure, and dissolved phosphorous concentration also played important role for the community structure. The CCA ordination plots could well display the phytoplankton’s community structure and its relationships with environmental factors.