Abstract: Dongjiang River lies in the subtropical monsoon climate region of the southern China. From December 2009 to September 2010, composition and seasonal succession of phytoplankton functional groups in the river were investigated during low, level and high water period, respectively. Altogether 14 functional groups (functional groups J, X2, P, W2, H1, MP, D, F, C, LO, W1, N, X1 and M) were identified and the predominant groups in the succession were groups J, X2, P, W2, H1, MP, D, F, C, LO and M. Functional groups composition in Dongjiang River demonstrated obviously seasonal dynamics. In low water period, the predominant functional groups were MP, D, P, X2, F, J and W2; however, the prevailing groups shifted to functional groups MP, J, LO and H1 in high water period. The succession of phytoplankton functional groups was also significantly correlated with physical factors-water temperature (WT), pH, dissolved oxygen (DO) and total dissolved solids content (TDS). This study indicated that the functional groups concept was also useful and applicable in demonstrating phytoplankton composition of river ecosystem.