Abstract: The surveys on phytoplankton community and physical-chemical environmental parameters were carried out in May, August and November 2016 and February 2017 to study the spatial and seasonal dynamic of the phytoplankton community structure and its relationship with the environmental factors in the Fangchenghe estuary (Guangxi, China). A total of 162 species of phytoplankton were identified, which consisted of 123 species in Bacillariophyta, 29 species in Pyrrophyta, 6 species in Chlorophyta, 3 species in Chrysophyta and 1 species in Cryptophyta, respectively. 104 species were found in spring, 86 species in summer, 93 species in autumn and 79 species in winter, respectively. The annual average cell density in the bay is 41.34×10⁴ cells/L. The highest was observed in autumn (100.18×10⁴ cells/L), in turn followed in spring (48.04×10⁴ cells/L), summer (16.03×10⁴ cells/L) and winter (1.11×10⁴ cells/L). The dominant species were composed of Chaetoceros pseudocurvisetus, Skeletonema costatum and Skeletonema tropicum, in which S. costatum ranked first in spring and summer, while C. pseudocurvisetus ranked first in autumn and winter, respectively. Species number (SN) ranged from 2 species to 17 species among stations, with the species diversity index (H′) from 0. 326 to 3. 918, the richness index (d) from 0. 782 to 3.789, and the evenness index (J) from 0.086 to 0.784. Seasonal alternation rates of dominant species varied from 50.0% to 88.9%, with alternation indexes of total species from 55.7% to 97.4%, and species migration indexes form −12.2% to 19.5%. Analysis of CLUSTER, similarity (ANOSIM) and similarity of percentage (SIMPER) showed that there were to some extent spatiotemporal heterogeneity for the phytoplankton community structure. Redundancy analysis showed that the major environmental factors determining the distribution pattern of phytoplankton communities in the bay were salinity in spring, ammonium and water depth in summer, total phosphorus in autumn, and dissolved oxygen, inorganic phosphorus, water color and water depth in winter, respectively.