Seasonal variation of primary productivity and its causing factors were investigated during the algae bloom period and dry season in the backwater area of the Daning River, a branch of the Three Gorges, China. The results indicate that most of the investigated physico-chemical parameters, including water temperature, DO concentration (saturation), SPC (specific conductivity), pH, TUR (Turbidity), etc., in the Daning River are significantly different between the algae bloom period and dry season （ANOVA，  p0.05）. The results suggest that primary productivity and chlorophyll-a in algae bloom period are higher than those in the dry season（ANOVA， p 0.05）. The vertical distribution of PG (Gross primary productivity)， PN (net production) and Chl-a(chlorophyll-a) were not significantly different. The maximum of chlorophyll-a concentrations were observed at 9 m underwater, and the maximun of PN 、 PG were observed from 0 m to 3 m underwater. The results indicate that the Daning River backwater area has a high spatial and temporal heterogeneity in the gross primary productivity， net production and chlorophyll-a. The maximun of gross primary productivity， net production and chlorophyll-a were observed from 0 m to 0.8 m underwater. The results suggest that the water temperature and turbidity are key regulatory factors for primary production. The changes of pH, DO concentration (saturation) and SPC may be the results of the change of the phy-toplankton.